/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.25mers.hg38-chr10.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.25mers.hg38-chr10.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.25mers.hg38-chr11.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.25mers.hg38-chr11.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.25mers.hg38-chr11_KI270721v1_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.25mers.hg38-chr11_KI270721v1_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.25mers.hg38-chr12.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.25mers.hg38-chr12.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.25mers.hg38-chr13.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.25mers.hg38-chr13.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.25mers.hg38-chr14.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.25mers.hg38-chr14.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.25mers.hg38-chr14_GL000009v2_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.25mers.hg38-chr14_GL000009v2_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.25mers.hg38-chr14_GL000194v1_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.25mers.hg38-chr14_GL000194v1_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.25mers.hg38-chr14_GL000225v1_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.25mers.hg38-chr14_GL000225v1_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.25mers.hg38-chr14_KI270722v1_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.25mers.hg38-chr14_KI270722v1_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.25mers.hg38-chr14_KI270723v1_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.25mers.hg38-chr14_KI270723v1_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.25mers.hg38-chr14_KI270724v1_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.25mers.hg38-chr14_KI270724v1_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.25mers.hg38-chr14_KI270725v1_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.25mers.hg38-chr14_KI270725v1_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.25mers.hg38-chr14_KI270726v1_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.25mers.hg38-chr14_KI270726v1_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.25mers.hg38-chr15.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.25mers.hg38-chr15.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.25mers.hg38-chr15_KI270727v1_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.25mers.hg38-chr15_KI270727v1_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.25mers.hg38-chr16.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.25mers.hg38-chr16.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.25mers.hg38-chr16_KI270728v1_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.25mers.hg38-chr16_KI270728v1_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.25mers.hg38-chr17.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.25mers.hg38-chr17.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.25mers.hg38-chr17_GL000205v2_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.25mers.hg38-chr17_GL000205v2_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.25mers.hg38-chr17_KI270729v1_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.25mers.hg38-chr17_KI270729v1_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.25mers.hg38-chr17_KI270730v1_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.25mers.hg38-chr17_KI270730v1_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.25mers.hg38-chr18.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.25mers.hg38-chr18.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.25mers.hg38-chr19.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.25mers.hg38-chr19.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.25mers.hg38-chr1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.25mers.hg38-chr1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.25mers.hg38-chr1_KI270706v1_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.25mers.hg38-chr1_KI270706v1_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.25mers.hg38-chr1_KI270707v1_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.25mers.hg38-chr1_KI270707v1_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.25mers.hg38-chr1_KI270708v1_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.25mers.hg38-chr1_KI270708v1_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.25mers.hg38-chr1_KI270709v1_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.25mers.hg38-chr1_KI270709v1_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.25mers.hg38-chr1_KI270710v1_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.25mers.hg38-chr1_KI270710v1_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.25mers.hg38-chr1_KI270711v1_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.25mers.hg38-chr1_KI270711v1_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.25mers.hg38-chr1_KI270712v1_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.25mers.hg38-chr1_KI270712v1_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.25mers.hg38-chr1_KI270713v1_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.25mers.hg38-chr1_KI270713v1_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.25mers.hg38-chr1_KI270714v1_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.25mers.hg38-chr1_KI270714v1_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.25mers.hg38-chr20.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.25mers.hg38-chr20.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.25mers.hg38-chr21.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.25mers.hg38-chr21.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.25mers.hg38-chr22.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.25mers.hg38-chr22.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.25mers.hg38-chr22_KI270731v1_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.25mers.hg38-chr22_KI270731v1_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.25mers.hg38-chr22_KI270732v1_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.25mers.hg38-chr22_KI270732v1_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.25mers.hg38-chr22_KI270733v1_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.25mers.hg38-chr22_KI270733v1_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.25mers.hg38-chr22_KI270734v1_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.25mers.hg38-chr22_KI270734v1_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.25mers.hg38-chr22_KI270735v1_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.25mers.hg38-chr22_KI270735v1_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.25mers.hg38-chr22_KI270736v1_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.25mers.hg38-chr22_KI270736v1_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.25mers.hg38-chr22_KI270737v1_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.25mers.hg38-chr22_KI270737v1_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.25mers.hg38-chr22_KI270738v1_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.25mers.hg38-chr22_KI270738v1_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.25mers.hg38-chr22_KI270739v1_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.25mers.hg38-chr22_KI270739v1_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.25mers.hg38-chr2.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.25mers.hg38-chr2.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.25mers.hg38-chr2_KI270715v1_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.25mers.hg38-chr2_KI270715v1_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.25mers.hg38-chr2_KI270716v1_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.25mers.hg38-chr2_KI270716v1_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.25mers.hg38-chr3.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.25mers.hg38-chr3.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.25mers.hg38-chr3_GL000221v1_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.25mers.hg38-chr3_GL000221v1_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.25mers.hg38-chr4.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.25mers.hg38-chr4.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.25mers.hg38-chr4_GL000008v2_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.25mers.hg38-chr4_GL000008v2_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.25mers.hg38-chr5.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.25mers.hg38-chr5.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.25mers.hg38-chr5_GL000208v1_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.25mers.hg38-chr5_GL000208v1_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.25mers.hg38-chr6.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.25mers.hg38-chr6.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.25mers.hg38-chr7.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.25mers.hg38-chr7.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.25mers.hg38-chr8.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.25mers.hg38-chr8.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.25mers.hg38-chr9.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.25mers.hg38-chr9.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.25mers.hg38-chr9_KI270717v1_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.25mers.hg38-chr9_KI270717v1_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.25mers.hg38-chr9_KI270718v1_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.25mers.hg38-chr9_KI270718v1_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.25mers.hg38-chr9_KI270719v1_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.25mers.hg38-chr9_KI270719v1_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.25mers.hg38-chr9_KI270720v1_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.25mers.hg38-chr9_KI270720v1_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.25mers.hg38-chrM.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.25mers.hg38-chrM.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.25mers.hg38-chrUn_GL000195v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.25mers.hg38-chrUn_GL000195v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.25mers.hg38-chrUn_GL000213v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.25mers.hg38-chrUn_GL000213v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.25mers.hg38-chrUn_GL000214v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.25mers.hg38-chrUn_GL000214v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.25mers.hg38-chrUn_GL000216v2.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.25mers.hg38-chrUn_GL000216v2.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.25mers.hg38-chrUn_GL000218v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.25mers.hg38-chrUn_GL000218v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.25mers.hg38-chrUn_GL000219v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.25mers.hg38-chrUn_GL000219v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.25mers.hg38-chrUn_GL000220v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.25mers.hg38-chrUn_GL000220v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.25mers.hg38-chrUn_GL000224v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.25mers.hg38-chrUn_GL000224v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.25mers.hg38-chrUn_GL000226v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.25mers.hg38-chrUn_GL000226v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.25mers.hg38-chrUn_KI270302v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.25mers.hg38-chrUn_KI270302v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.25mers.hg38-chrUn_KI270303v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.25mers.hg38-chrUn_KI270303v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.25mers.hg38-chrUn_KI270304v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.25mers.hg38-chrUn_KI270304v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.25mers.hg38-chrUn_KI270305v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.25mers.hg38-chrUn_KI270305v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.25mers.hg38-chrUn_KI270310v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.25mers.hg38-chrUn_KI270310v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.25mers.hg38-chrUn_KI270311v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.25mers.hg38-chrUn_KI270311v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.25mers.hg38-chrUn_KI270312v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.25mers.hg38-chrUn_KI270312v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.25mers.hg38-chrUn_KI270315v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.25mers.hg38-chrUn_KI270315v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.25mers.hg38-chrUn_KI270316v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.25mers.hg38-chrUn_KI270316v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.25mers.hg38-chrUn_KI270317v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.25mers.hg38-chrUn_KI270317v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.25mers.hg38-chrUn_KI270320v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.25mers.hg38-chrUn_KI270320v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.25mers.hg38-chrUn_KI270322v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.25mers.hg38-chrUn_KI270322v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.25mers.hg38-chrUn_KI270329v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.25mers.hg38-chrUn_KI270329v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.25mers.hg38-chrUn_KI270330v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.25mers.hg38-chrUn_KI270330v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.25mers.hg38-chrUn_KI270333v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.25mers.hg38-chrUn_KI270333v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.25mers.hg38-chrUn_KI270334v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.25mers.hg38-chrUn_KI270334v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.25mers.hg38-chrUn_KI270335v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.25mers.hg38-chrUn_KI270335v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.25mers.hg38-chrUn_KI270336v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.25mers.hg38-chrUn_KI270336v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.25mers.hg38-chrUn_KI270337v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.25mers.hg38-chrUn_KI270337v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.25mers.hg38-chrUn_KI270338v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.25mers.hg38-chrUn_KI270338v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.25mers.hg38-chrUn_KI270340v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.25mers.hg38-chrUn_KI270340v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.25mers.hg38-chrUn_KI270362v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.25mers.hg38-chrUn_KI270362v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.25mers.hg38-chrUn_KI270363v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.25mers.hg38-chrUn_KI270363v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.25mers.hg38-chrUn_KI270364v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.25mers.hg38-chrUn_KI270364v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.25mers.hg38-chrUn_KI270366v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.25mers.hg38-chrUn_KI270366v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.25mers.hg38-chrUn_KI270371v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.25mers.hg38-chrUn_KI270371v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.25mers.hg38-chrUn_KI270372v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.25mers.hg38-chrUn_KI270372v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.25mers.hg38-chrUn_KI270373v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.25mers.hg38-chrUn_KI270373v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.25mers.hg38-chrUn_KI270374v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.25mers.hg38-chrUn_KI270374v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.25mers.hg38-chrUn_KI270375v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.25mers.hg38-chrUn_KI270375v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.25mers.hg38-chrUn_KI270376v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.25mers.hg38-chrUn_KI270376v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.25mers.hg38-chrUn_KI270378v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.25mers.hg38-chrUn_KI270378v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.25mers.hg38-chrUn_KI270379v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.25mers.hg38-chrUn_KI270379v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.25mers.hg38-chrUn_KI270381v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.25mers.hg38-chrUn_KI270381v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.25mers.hg38-chrUn_KI270382v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.25mers.hg38-chrUn_KI270382v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.25mers.hg38-chrUn_KI270383v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.25mers.hg38-chrUn_KI270383v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.25mers.hg38-chrUn_KI270384v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.25mers.hg38-chrUn_KI270384v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.25mers.hg38-chrUn_KI270385v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.25mers.hg38-chrUn_KI270385v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.25mers.hg38-chrUn_KI270386v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.25mers.hg38-chrUn_KI270386v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.25mers.hg38-chrUn_KI270387v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.25mers.hg38-chrUn_KI270387v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.25mers.hg38-chrUn_KI270388v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.25mers.hg38-chrUn_KI270388v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.25mers.hg38-chrUn_KI270389v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.25mers.hg38-chrUn_KI270389v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.25mers.hg38-chrUn_KI270390v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.25mers.hg38-chrUn_KI270390v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.25mers.hg38-chrUn_KI270391v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.25mers.hg38-chrUn_KI270391v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.25mers.hg38-chrUn_KI270392v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.25mers.hg38-chrUn_KI270392v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.25mers.hg38-chrUn_KI270393v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.25mers.hg38-chrUn_KI270393v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.25mers.hg38-chrUn_KI270394v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.25mers.hg38-chrUn_KI270394v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.25mers.hg38-chrUn_KI270395v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.25mers.hg38-chrUn_KI270395v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.25mers.hg38-chrUn_KI270396v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.25mers.hg38-chrUn_KI270396v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.25mers.hg38-chrUn_KI270411v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.25mers.hg38-chrUn_KI270411v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.25mers.hg38-chrUn_KI270412v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.25mers.hg38-chrUn_KI270412v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.25mers.hg38-chrUn_KI270414v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.25mers.hg38-chrUn_KI270414v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.25mers.hg38-chrUn_KI270417v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.25mers.hg38-chrUn_KI270417v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.25mers.hg38-chrUn_KI270418v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.25mers.hg38-chrUn_KI270418v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.25mers.hg38-chrUn_KI270419v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.25mers.hg38-chrUn_KI270419v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.25mers.hg38-chrUn_KI270420v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.25mers.hg38-chrUn_KI270420v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.25mers.hg38-chrUn_KI270422v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.25mers.hg38-chrUn_KI270422v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.25mers.hg38-chrUn_KI270423v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.25mers.hg38-chrUn_KI270423v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.25mers.hg38-chrUn_KI270424v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.25mers.hg38-chrUn_KI270424v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.25mers.hg38-chrUn_KI270425v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.25mers.hg38-chrUn_KI270425v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.25mers.hg38-chrUn_KI270429v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.25mers.hg38-chrUn_KI270429v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.25mers.hg38-chrUn_KI270435v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.25mers.hg38-chrUn_KI270435v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.25mers.hg38-chrUn_KI270438v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.25mers.hg38-chrUn_KI270438v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.25mers.hg38-chrUn_KI270442v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.25mers.hg38-chrUn_KI270442v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.25mers.hg38-chrUn_KI270448v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.25mers.hg38-chrUn_KI270448v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.25mers.hg38-chrUn_KI270465v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.25mers.hg38-chrUn_KI270465v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.25mers.hg38-chrUn_KI270466v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.25mers.hg38-chrUn_KI270466v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.25mers.hg38-chrUn_KI270467v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.25mers.hg38-chrUn_KI270467v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.25mers.hg38-chrUn_KI270468v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.25mers.hg38-chrUn_KI270468v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.25mers.hg38-chrUn_KI270507v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.25mers.hg38-chrUn_KI270507v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.25mers.hg38-chrUn_KI270508v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.25mers.hg38-chrUn_KI270508v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.25mers.hg38-chrUn_KI270509v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.25mers.hg38-chrUn_KI270509v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.25mers.hg38-chrUn_KI270510v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.25mers.hg38-chrUn_KI270510v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.25mers.hg38-chrUn_KI270511v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.25mers.hg38-chrUn_KI270511v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.25mers.hg38-chrUn_KI270512v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.25mers.hg38-chrUn_KI270512v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.25mers.hg38-chrUn_KI270515v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.25mers.hg38-chrUn_KI270515v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.25mers.hg38-chrUn_KI270516v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.25mers.hg38-chrUn_KI270516v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.25mers.hg38-chrUn_KI270517v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.25mers.hg38-chrUn_KI270517v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.25mers.hg38-chrUn_KI270518v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.25mers.hg38-chrUn_KI270518v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.25mers.hg38-chrUn_KI270519v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.25mers.hg38-chrUn_KI270519v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.25mers.hg38-chrUn_KI270521v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.25mers.hg38-chrUn_KI270521v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.25mers.hg38-chrUn_KI270522v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.25mers.hg38-chrUn_KI270522v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.25mers.hg38-chrUn_KI270528v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.25mers.hg38-chrUn_KI270528v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.25mers.hg38-chrUn_KI270529v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.25mers.hg38-chrUn_KI270529v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.25mers.hg38-chrUn_KI270530v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.25mers.hg38-chrUn_KI270530v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.25mers.hg38-chrUn_KI270538v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.25mers.hg38-chrUn_KI270538v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.25mers.hg38-chrUn_KI270539v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.25mers.hg38-chrUn_KI270539v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.25mers.hg38-chrUn_KI270544v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.25mers.hg38-chrUn_KI270544v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.25mers.hg38-chrUn_KI270548v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.25mers.hg38-chrUn_KI270548v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.25mers.hg38-chrUn_KI270579v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.25mers.hg38-chrUn_KI270579v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.25mers.hg38-chrUn_KI270580v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.25mers.hg38-chrUn_KI270580v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.25mers.hg38-chrUn_KI270581v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.25mers.hg38-chrUn_KI270581v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.25mers.hg38-chrUn_KI270582v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.25mers.hg38-chrUn_KI270582v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.25mers.hg38-chrUn_KI270583v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.25mers.hg38-chrUn_KI270583v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.25mers.hg38-chrUn_KI270584v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.25mers.hg38-chrUn_KI270584v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.25mers.hg38-chrUn_KI270587v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.25mers.hg38-chrUn_KI270587v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.25mers.hg38-chrUn_KI270588v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.25mers.hg38-chrUn_KI270588v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.25mers.hg38-chrUn_KI270589v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.25mers.hg38-chrUn_KI270589v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.25mers.hg38-chrUn_KI270590v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.25mers.hg38-chrUn_KI270590v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.25mers.hg38-chrUn_KI270591v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.25mers.hg38-chrUn_KI270591v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.25mers.hg38-chrUn_KI270593v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.25mers.hg38-chrUn_KI270593v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.25mers.hg38-chrUn_KI270741v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.25mers.hg38-chrUn_KI270741v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.25mers.hg38-chrUn_KI270742v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.25mers.hg38-chrUn_KI270742v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.25mers.hg38-chrUn_KI270743v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.25mers.hg38-chrUn_KI270743v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.25mers.hg38-chrUn_KI270744v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.25mers.hg38-chrUn_KI270744v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.25mers.hg38-chrUn_KI270745v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.25mers.hg38-chrUn_KI270745v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.25mers.hg38-chrUn_KI270746v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.25mers.hg38-chrUn_KI270746v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.25mers.hg38-chrUn_KI270747v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.25mers.hg38-chrUn_KI270747v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.25mers.hg38-chrUn_KI270748v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.25mers.hg38-chrUn_KI270748v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.25mers.hg38-chrUn_KI270749v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.25mers.hg38-chrUn_KI270749v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.25mers.hg38-chrUn_KI270750v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.25mers.hg38-chrUn_KI270750v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.25mers.hg38-chrUn_KI270751v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.25mers.hg38-chrUn_KI270751v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.25mers.hg38-chrUn_KI270752v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.25mers.hg38-chrUn_KI270752v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.25mers.hg38-chrUn_KI270753v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.25mers.hg38-chrUn_KI270753v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.25mers.hg38-chrUn_KI270754v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.25mers.hg38-chrUn_KI270754v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.25mers.hg38-chrUn_KI270755v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.25mers.hg38-chrUn_KI270755v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.25mers.hg38-chrUn_KI270756v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.25mers.hg38-chrUn_KI270756v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.25mers.hg38-chrUn_KI270757v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.25mers.hg38-chrUn_KI270757v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.25mers.hg38-chrX.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.25mers.hg38-chrX.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.25mers.hg38-chrY.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.25mers.hg38-chrY.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.25mers.hg38-chrY_KI270740v1_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.25mers.hg38-chrY_KI270740v1_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.25mers.mm10-chr10.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.25mers.mm10-chr10.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.25mers.mm10-chr11.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.25mers.mm10-chr11.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.25mers.mm10-chr12.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.25mers.mm10-chr12.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.25mers.mm10-chr13.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.25mers.mm10-chr13.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.25mers.mm10-chr14.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.25mers.mm10-chr14.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.25mers.mm10-chr15.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.25mers.mm10-chr15.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.25mers.mm10-chr16.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.25mers.mm10-chr16.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.25mers.mm10-chr17.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.25mers.mm10-chr17.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.25mers.mm10-chr18.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.25mers.mm10-chr18.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.25mers.mm10-chr19.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.25mers.mm10-chr19.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.25mers.mm10-chr1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.25mers.mm10-chr1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.25mers.mm10-chr1_GL456210_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.25mers.mm10-chr1_GL456210_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.25mers.mm10-chr1_GL456211_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.25mers.mm10-chr1_GL456211_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.25mers.mm10-chr1_GL456212_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.25mers.mm10-chr1_GL456212_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.25mers.mm10-chr1_GL456213_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.25mers.mm10-chr1_GL456213_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.25mers.mm10-chr1_GL456221_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.25mers.mm10-chr1_GL456221_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.25mers.mm10-chr2.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.25mers.mm10-chr2.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.25mers.mm10-chr3.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.25mers.mm10-chr3.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.25mers.mm10-chr4.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.25mers.mm10-chr4.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.25mers.mm10-chr4_GL456216_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.25mers.mm10-chr4_GL456216_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.25mers.mm10-chr4_GL456350_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.25mers.mm10-chr4_GL456350_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.25mers.mm10-chr4_JH584292_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.25mers.mm10-chr4_JH584292_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.25mers.mm10-chr4_JH584293_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.25mers.mm10-chr4_JH584293_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.25mers.mm10-chr4_JH584294_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.25mers.mm10-chr4_JH584294_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.25mers.mm10-chr4_JH584295_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.25mers.mm10-chr4_JH584295_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.25mers.mm10-chr5.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.25mers.mm10-chr5.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.25mers.mm10-chr5_GL456354_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.25mers.mm10-chr5_GL456354_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.25mers.mm10-chr5_JH584296_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.25mers.mm10-chr5_JH584296_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.25mers.mm10-chr5_JH584297_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.25mers.mm10-chr5_JH584297_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.25mers.mm10-chr5_JH584298_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.25mers.mm10-chr5_JH584298_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.25mers.mm10-chr5_JH584299_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.25mers.mm10-chr5_JH584299_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.25mers.mm10-chr6.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.25mers.mm10-chr6.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.25mers.mm10-chr7.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.25mers.mm10-chr7.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.25mers.mm10-chr7_GL456219_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.25mers.mm10-chr7_GL456219_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.25mers.mm10-chr8.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.25mers.mm10-chr8.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.25mers.mm10-chr9.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.25mers.mm10-chr9.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.25mers.mm10-chrM.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.25mers.mm10-chrM.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.25mers.mm10-chrUn_GL456239.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.25mers.mm10-chrUn_GL456239.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.25mers.mm10-chrUn_GL456359.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.25mers.mm10-chrUn_GL456359.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.25mers.mm10-chrUn_GL456360.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.25mers.mm10-chrUn_GL456360.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.25mers.mm10-chrUn_GL456366.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.25mers.mm10-chrUn_GL456366.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.25mers.mm10-chrUn_GL456367.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.25mers.mm10-chrUn_GL456367.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.25mers.mm10-chrUn_GL456368.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.25mers.mm10-chrUn_GL456368.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.25mers.mm10-chrUn_GL456370.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.25mers.mm10-chrUn_GL456370.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.25mers.mm10-chrUn_GL456372.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.25mers.mm10-chrUn_GL456372.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.25mers.mm10-chrUn_GL456378.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.25mers.mm10-chrUn_GL456378.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.25mers.mm10-chrUn_GL456379.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.25mers.mm10-chrUn_GL456379.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.25mers.mm10-chrUn_GL456381.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.25mers.mm10-chrUn_GL456381.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.25mers.mm10-chrUn_GL456382.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.25mers.mm10-chrUn_GL456382.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.25mers.mm10-chrUn_GL456383.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.25mers.mm10-chrUn_GL456383.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.25mers.mm10-chrUn_GL456385.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.25mers.mm10-chrUn_GL456385.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.25mers.mm10-chrUn_GL456387.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.25mers.mm10-chrUn_GL456387.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.25mers.mm10-chrUn_GL456389.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.25mers.mm10-chrUn_GL456389.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.25mers.mm10-chrUn_GL456390.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.25mers.mm10-chrUn_GL456390.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.25mers.mm10-chrUn_GL456392.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.25mers.mm10-chrUn_GL456392.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.25mers.mm10-chrUn_GL456393.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.25mers.mm10-chrUn_GL456393.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.25mers.mm10-chrUn_GL456394.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.25mers.mm10-chrUn_GL456394.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.25mers.mm10-chrUn_GL456396.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.25mers.mm10-chrUn_GL456396.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.25mers.mm10-chrUn_JH584304.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.25mers.mm10-chrUn_JH584304.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.25mers.mm10-chrX.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.25mers.mm10-chrX.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.25mers.mm10-chrX_GL456233_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.25mers.mm10-chrX_GL456233_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.25mers.mm10-chrY.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.25mers.mm10-chrY.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.25mers.mm10-chrY_JH584300_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.25mers.mm10-chrY_JH584300_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.25mers.mm10-chrY_JH584301_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.25mers.mm10-chrY_JH584301_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.25mers.mm10-chrY_JH584302_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.25mers.mm10-chrY_JH584302_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.25mers.mm10-chrY_JH584303_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.25mers.mm10-chrY_JH584303_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.36mers.hg38-chr10.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.36mers.hg38-chr10.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.36mers.hg38-chr11.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.36mers.hg38-chr11.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.36mers.hg38-chr11_KI270721v1_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.36mers.hg38-chr11_KI270721v1_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.36mers.hg38-chr12.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.36mers.hg38-chr12.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.36mers.hg38-chr13.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.36mers.hg38-chr13.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.36mers.hg38-chr14.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.36mers.hg38-chr14.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.36mers.hg38-chr14_GL000009v2_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.36mers.hg38-chr14_GL000009v2_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.36mers.hg38-chr14_GL000194v1_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.36mers.hg38-chr14_GL000194v1_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.36mers.hg38-chr14_GL000225v1_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.36mers.hg38-chr14_GL000225v1_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.36mers.hg38-chr14_KI270722v1_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.36mers.hg38-chr14_KI270722v1_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.36mers.hg38-chr14_KI270723v1_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.36mers.hg38-chr14_KI270723v1_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.36mers.hg38-chr14_KI270724v1_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.36mers.hg38-chr14_KI270724v1_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.36mers.hg38-chr14_KI270725v1_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.36mers.hg38-chr14_KI270725v1_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.36mers.hg38-chr14_KI270726v1_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.36mers.hg38-chr14_KI270726v1_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.36mers.hg38-chr15.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.36mers.hg38-chr15.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.36mers.hg38-chr15_KI270727v1_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.36mers.hg38-chr15_KI270727v1_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.36mers.hg38-chr16.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.36mers.hg38-chr16.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.36mers.hg38-chr16_KI270728v1_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.36mers.hg38-chr16_KI270728v1_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.36mers.hg38-chr17.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.36mers.hg38-chr17.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.36mers.hg38-chr17_GL000205v2_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.36mers.hg38-chr17_GL000205v2_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.36mers.hg38-chr17_KI270729v1_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.36mers.hg38-chr17_KI270729v1_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.36mers.hg38-chr17_KI270730v1_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.36mers.hg38-chr17_KI270730v1_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.36mers.hg38-chr18.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.36mers.hg38-chr18.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.36mers.hg38-chr19.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.36mers.hg38-chr19.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.36mers.hg38-chr1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.36mers.hg38-chr1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.36mers.hg38-chr1_KI270706v1_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.36mers.hg38-chr1_KI270706v1_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.36mers.hg38-chr1_KI270707v1_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.36mers.hg38-chr1_KI270707v1_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.36mers.hg38-chr1_KI270708v1_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.36mers.hg38-chr1_KI270708v1_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.36mers.hg38-chr1_KI270709v1_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.36mers.hg38-chr1_KI270709v1_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.36mers.hg38-chr1_KI270710v1_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.36mers.hg38-chr1_KI270710v1_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.36mers.hg38-chr1_KI270711v1_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.36mers.hg38-chr1_KI270711v1_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.36mers.hg38-chr1_KI270712v1_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.36mers.hg38-chr1_KI270712v1_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.36mers.hg38-chr1_KI270713v1_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.36mers.hg38-chr1_KI270713v1_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.36mers.hg38-chr1_KI270714v1_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.36mers.hg38-chr1_KI270714v1_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.36mers.hg38-chr20.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.36mers.hg38-chr20.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.36mers.hg38-chr21.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.36mers.hg38-chr21.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.36mers.hg38-chr22.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.36mers.hg38-chr22.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.36mers.hg38-chr22_KI270731v1_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.36mers.hg38-chr22_KI270731v1_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.36mers.hg38-chr22_KI270732v1_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.36mers.hg38-chr22_KI270732v1_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.36mers.hg38-chr22_KI270733v1_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.36mers.hg38-chr22_KI270733v1_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.36mers.hg38-chr22_KI270734v1_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.36mers.hg38-chr22_KI270734v1_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.36mers.hg38-chr22_KI270735v1_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.36mers.hg38-chr22_KI270735v1_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.36mers.hg38-chr22_KI270736v1_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.36mers.hg38-chr22_KI270736v1_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.36mers.hg38-chr22_KI270737v1_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.36mers.hg38-chr22_KI270737v1_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.36mers.hg38-chr22_KI270738v1_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.36mers.hg38-chr22_KI270738v1_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.36mers.hg38-chr22_KI270739v1_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.36mers.hg38-chr22_KI270739v1_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.36mers.hg38-chr2.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.36mers.hg38-chr2.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.36mers.hg38-chr2_KI270715v1_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.36mers.hg38-chr2_KI270715v1_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.36mers.hg38-chr2_KI270716v1_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.36mers.hg38-chr2_KI270716v1_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.36mers.hg38-chr3.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.36mers.hg38-chr3.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.36mers.hg38-chr3_GL000221v1_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.36mers.hg38-chr3_GL000221v1_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.36mers.hg38-chr4.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.36mers.hg38-chr4.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.36mers.hg38-chr4_GL000008v2_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.36mers.hg38-chr4_GL000008v2_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.36mers.hg38-chr5.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.36mers.hg38-chr5.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.36mers.hg38-chr5_GL000208v1_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.36mers.hg38-chr5_GL000208v1_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.36mers.hg38-chr6.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.36mers.hg38-chr6.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.36mers.hg38-chr7.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.36mers.hg38-chr7.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.36mers.hg38-chr8.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.36mers.hg38-chr8.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.36mers.hg38-chr9.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.36mers.hg38-chr9.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.36mers.hg38-chr9_KI270717v1_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.36mers.hg38-chr9_KI270717v1_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.36mers.hg38-chr9_KI270718v1_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.36mers.hg38-chr9_KI270718v1_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.36mers.hg38-chr9_KI270719v1_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.36mers.hg38-chr9_KI270719v1_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.36mers.hg38-chr9_KI270720v1_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.36mers.hg38-chr9_KI270720v1_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.36mers.hg38-chrM.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.36mers.hg38-chrM.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.36mers.hg38-chrUn_GL000195v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.36mers.hg38-chrUn_GL000195v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.36mers.hg38-chrUn_GL000213v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.36mers.hg38-chrUn_GL000213v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.36mers.hg38-chrUn_GL000214v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.36mers.hg38-chrUn_GL000214v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.36mers.hg38-chrUn_GL000216v2.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.36mers.hg38-chrUn_GL000216v2.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.36mers.hg38-chrUn_GL000218v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.36mers.hg38-chrUn_GL000218v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.36mers.hg38-chrUn_GL000219v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.36mers.hg38-chrUn_GL000219v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.36mers.hg38-chrUn_GL000220v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.36mers.hg38-chrUn_GL000220v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.36mers.hg38-chrUn_GL000224v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.36mers.hg38-chrUn_GL000224v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.36mers.hg38-chrUn_GL000226v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.36mers.hg38-chrUn_GL000226v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.36mers.hg38-chrUn_KI270302v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.36mers.hg38-chrUn_KI270302v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.36mers.hg38-chrUn_KI270303v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.36mers.hg38-chrUn_KI270303v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.36mers.hg38-chrUn_KI270304v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.36mers.hg38-chrUn_KI270304v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.36mers.hg38-chrUn_KI270305v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.36mers.hg38-chrUn_KI270305v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.36mers.hg38-chrUn_KI270310v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.36mers.hg38-chrUn_KI270310v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.36mers.hg38-chrUn_KI270311v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.36mers.hg38-chrUn_KI270311v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.36mers.hg38-chrUn_KI270312v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.36mers.hg38-chrUn_KI270312v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.36mers.hg38-chrUn_KI270315v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.36mers.hg38-chrUn_KI270315v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.36mers.hg38-chrUn_KI270316v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.36mers.hg38-chrUn_KI270316v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.36mers.hg38-chrUn_KI270317v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.36mers.hg38-chrUn_KI270317v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.36mers.hg38-chrUn_KI270320v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.36mers.hg38-chrUn_KI270320v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.36mers.hg38-chrUn_KI270322v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.36mers.hg38-chrUn_KI270322v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.36mers.hg38-chrUn_KI270329v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.36mers.hg38-chrUn_KI270329v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.36mers.hg38-chrUn_KI270330v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.36mers.hg38-chrUn_KI270330v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.36mers.hg38-chrUn_KI270333v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.36mers.hg38-chrUn_KI270333v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.36mers.hg38-chrUn_KI270334v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.36mers.hg38-chrUn_KI270334v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.36mers.hg38-chrUn_KI270335v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.36mers.hg38-chrUn_KI270335v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.36mers.hg38-chrUn_KI270336v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.36mers.hg38-chrUn_KI270336v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.36mers.hg38-chrUn_KI270337v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.36mers.hg38-chrUn_KI270337v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.36mers.hg38-chrUn_KI270338v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.36mers.hg38-chrUn_KI270338v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.36mers.hg38-chrUn_KI270340v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.36mers.hg38-chrUn_KI270340v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.36mers.hg38-chrUn_KI270362v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.36mers.hg38-chrUn_KI270362v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.36mers.hg38-chrUn_KI270363v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.36mers.hg38-chrUn_KI270363v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.36mers.hg38-chrUn_KI270364v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.36mers.hg38-chrUn_KI270364v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.36mers.hg38-chrUn_KI270366v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.36mers.hg38-chrUn_KI270366v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.36mers.hg38-chrUn_KI270371v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.36mers.hg38-chrUn_KI270371v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.36mers.hg38-chrUn_KI270372v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.36mers.hg38-chrUn_KI270372v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.36mers.hg38-chrUn_KI270373v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.36mers.hg38-chrUn_KI270373v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.36mers.hg38-chrUn_KI270374v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.36mers.hg38-chrUn_KI270374v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.36mers.hg38-chrUn_KI270375v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.36mers.hg38-chrUn_KI270375v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.36mers.hg38-chrUn_KI270376v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.36mers.hg38-chrUn_KI270376v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.36mers.hg38-chrUn_KI270378v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.36mers.hg38-chrUn_KI270378v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.36mers.hg38-chrUn_KI270379v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.36mers.hg38-chrUn_KI270379v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.36mers.hg38-chrUn_KI270381v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.36mers.hg38-chrUn_KI270381v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.36mers.hg38-chrUn_KI270382v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.36mers.hg38-chrUn_KI270382v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.36mers.hg38-chrUn_KI270383v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.36mers.hg38-chrUn_KI270383v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.36mers.hg38-chrUn_KI270384v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.36mers.hg38-chrUn_KI270384v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.36mers.hg38-chrUn_KI270385v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.36mers.hg38-chrUn_KI270385v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.36mers.hg38-chrUn_KI270386v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.36mers.hg38-chrUn_KI270386v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.36mers.hg38-chrUn_KI270387v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.36mers.hg38-chrUn_KI270387v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.36mers.hg38-chrUn_KI270388v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.36mers.hg38-chrUn_KI270388v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.36mers.hg38-chrUn_KI270389v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.36mers.hg38-chrUn_KI270389v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.36mers.hg38-chrUn_KI270390v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.36mers.hg38-chrUn_KI270390v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.36mers.hg38-chrUn_KI270391v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.36mers.hg38-chrUn_KI270391v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.36mers.hg38-chrUn_KI270392v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.36mers.hg38-chrUn_KI270392v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.36mers.hg38-chrUn_KI270393v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.36mers.hg38-chrUn_KI270393v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.36mers.hg38-chrUn_KI270394v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.36mers.hg38-chrUn_KI270394v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.36mers.hg38-chrUn_KI270395v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.36mers.hg38-chrUn_KI270395v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.36mers.hg38-chrUn_KI270396v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.36mers.hg38-chrUn_KI270396v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.36mers.hg38-chrUn_KI270411v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.36mers.hg38-chrUn_KI270411v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.36mers.hg38-chrUn_KI270412v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.36mers.hg38-chrUn_KI270412v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.36mers.hg38-chrUn_KI270414v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.36mers.hg38-chrUn_KI270414v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.36mers.hg38-chrUn_KI270417v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.36mers.hg38-chrUn_KI270417v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.36mers.hg38-chrUn_KI270418v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.36mers.hg38-chrUn_KI270418v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.36mers.hg38-chrUn_KI270419v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.36mers.hg38-chrUn_KI270419v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.36mers.hg38-chrUn_KI270420v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.36mers.hg38-chrUn_KI270420v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.36mers.hg38-chrUn_KI270422v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.36mers.hg38-chrUn_KI270422v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.36mers.hg38-chrUn_KI270423v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.36mers.hg38-chrUn_KI270423v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.36mers.hg38-chrUn_KI270424v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.36mers.hg38-chrUn_KI270424v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.36mers.hg38-chrUn_KI270425v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.36mers.hg38-chrUn_KI270425v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.36mers.hg38-chrUn_KI270429v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.36mers.hg38-chrUn_KI270429v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.36mers.hg38-chrUn_KI270435v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.36mers.hg38-chrUn_KI270435v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.36mers.hg38-chrUn_KI270438v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.36mers.hg38-chrUn_KI270438v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.36mers.hg38-chrUn_KI270442v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.36mers.hg38-chrUn_KI270442v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.36mers.hg38-chrUn_KI270448v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.36mers.hg38-chrUn_KI270448v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.36mers.hg38-chrUn_KI270465v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.36mers.hg38-chrUn_KI270465v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.36mers.hg38-chrUn_KI270466v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.36mers.hg38-chrUn_KI270466v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.36mers.hg38-chrUn_KI270467v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.36mers.hg38-chrUn_KI270467v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.36mers.hg38-chrUn_KI270468v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.36mers.hg38-chrUn_KI270468v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.36mers.hg38-chrUn_KI270507v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.36mers.hg38-chrUn_KI270507v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.36mers.hg38-chrUn_KI270508v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.36mers.hg38-chrUn_KI270508v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.36mers.hg38-chrUn_KI270509v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.36mers.hg38-chrUn_KI270509v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.36mers.hg38-chrUn_KI270510v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.36mers.hg38-chrUn_KI270510v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.36mers.hg38-chrUn_KI270511v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.36mers.hg38-chrUn_KI270511v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.36mers.hg38-chrUn_KI270512v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.36mers.hg38-chrUn_KI270512v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.36mers.hg38-chrUn_KI270515v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.36mers.hg38-chrUn_KI270515v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.36mers.hg38-chrUn_KI270516v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.36mers.hg38-chrUn_KI270516v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.36mers.hg38-chrUn_KI270517v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.36mers.hg38-chrUn_KI270517v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.36mers.hg38-chrUn_KI270518v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.36mers.hg38-chrUn_KI270518v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.36mers.hg38-chrUn_KI270519v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.36mers.hg38-chrUn_KI270519v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.36mers.hg38-chrUn_KI270521v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.36mers.hg38-chrUn_KI270521v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.36mers.hg38-chrUn_KI270522v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.36mers.hg38-chrUn_KI270522v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.36mers.hg38-chrUn_KI270528v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.36mers.hg38-chrUn_KI270528v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.36mers.hg38-chrUn_KI270529v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.36mers.hg38-chrUn_KI270529v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.36mers.hg38-chrUn_KI270530v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.36mers.hg38-chrUn_KI270530v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.36mers.hg38-chrUn_KI270538v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.36mers.hg38-chrUn_KI270538v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.36mers.hg38-chrUn_KI270539v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.36mers.hg38-chrUn_KI270539v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.36mers.hg38-chrUn_KI270544v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.36mers.hg38-chrUn_KI270544v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.36mers.hg38-chrUn_KI270548v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.36mers.hg38-chrUn_KI270548v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.36mers.hg38-chrUn_KI270579v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.36mers.hg38-chrUn_KI270579v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.36mers.hg38-chrUn_KI270580v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.36mers.hg38-chrUn_KI270580v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.36mers.hg38-chrUn_KI270581v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.36mers.hg38-chrUn_KI270581v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.36mers.hg38-chrUn_KI270582v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.36mers.hg38-chrUn_KI270582v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.36mers.hg38-chrUn_KI270583v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.36mers.hg38-chrUn_KI270583v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.36mers.hg38-chrUn_KI270584v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.36mers.hg38-chrUn_KI270584v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.36mers.hg38-chrUn_KI270587v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.36mers.hg38-chrUn_KI270587v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.36mers.hg38-chrUn_KI270588v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.36mers.hg38-chrUn_KI270588v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.36mers.hg38-chrUn_KI270589v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.36mers.hg38-chrUn_KI270589v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.36mers.hg38-chrUn_KI270590v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.36mers.hg38-chrUn_KI270590v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.36mers.hg38-chrUn_KI270591v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.36mers.hg38-chrUn_KI270591v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.36mers.hg38-chrUn_KI270593v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.36mers.hg38-chrUn_KI270593v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.36mers.hg38-chrUn_KI270741v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.36mers.hg38-chrUn_KI270741v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.36mers.hg38-chrUn_KI270742v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.36mers.hg38-chrUn_KI270742v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.36mers.hg38-chrUn_KI270743v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.36mers.hg38-chrUn_KI270743v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.36mers.hg38-chrUn_KI270744v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.36mers.hg38-chrUn_KI270744v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.36mers.hg38-chrUn_KI270745v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.36mers.hg38-chrUn_KI270745v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.36mers.hg38-chrUn_KI270746v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.36mers.hg38-chrUn_KI270746v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.36mers.hg38-chrUn_KI270747v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.36mers.hg38-chrUn_KI270747v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.36mers.hg38-chrUn_KI270748v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.36mers.hg38-chrUn_KI270748v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.36mers.hg38-chrUn_KI270749v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.36mers.hg38-chrUn_KI270749v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.36mers.hg38-chrUn_KI270750v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.36mers.hg38-chrUn_KI270750v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.36mers.hg38-chrUn_KI270751v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.36mers.hg38-chrUn_KI270751v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.36mers.hg38-chrUn_KI270752v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.36mers.hg38-chrUn_KI270752v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.36mers.hg38-chrUn_KI270753v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.36mers.hg38-chrUn_KI270753v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.36mers.hg38-chrUn_KI270754v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.36mers.hg38-chrUn_KI270754v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.36mers.hg38-chrUn_KI270755v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.36mers.hg38-chrUn_KI270755v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.36mers.hg38-chrUn_KI270756v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.36mers.hg38-chrUn_KI270756v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.36mers.hg38-chrUn_KI270757v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.36mers.hg38-chrUn_KI270757v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.36mers.hg38-chrX.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.36mers.hg38-chrX.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.36mers.hg38-chrY.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.36mers.hg38-chrY.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.36mers.hg38-chrY_KI270740v1_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.36mers.hg38-chrY_KI270740v1_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.36mers.mm10-chr10.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.36mers.mm10-chr10.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.36mers.mm10-chr11.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.36mers.mm10-chr11.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.36mers.mm10-chr12.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.36mers.mm10-chr12.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.36mers.mm10-chr13.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.36mers.mm10-chr13.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.36mers.mm10-chr14.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.36mers.mm10-chr14.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.36mers.mm10-chr15.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.36mers.mm10-chr15.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.36mers.mm10-chr16.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.36mers.mm10-chr16.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.36mers.mm10-chr17.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.36mers.mm10-chr17.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.36mers.mm10-chr18.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.36mers.mm10-chr18.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.36mers.mm10-chr19.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.36mers.mm10-chr19.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.36mers.mm10-chr1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.36mers.mm10-chr1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.36mers.mm10-chr1_GL456210_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.36mers.mm10-chr1_GL456210_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.36mers.mm10-chr1_GL456211_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.36mers.mm10-chr1_GL456211_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.36mers.mm10-chr1_GL456212_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.36mers.mm10-chr1_GL456212_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.36mers.mm10-chr1_GL456213_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.36mers.mm10-chr1_GL456213_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.36mers.mm10-chr1_GL456221_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.36mers.mm10-chr1_GL456221_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.36mers.mm10-chr2.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.36mers.mm10-chr2.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.36mers.mm10-chr3.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.36mers.mm10-chr3.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.36mers.mm10-chr4.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.36mers.mm10-chr4.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.36mers.mm10-chr4_GL456216_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.36mers.mm10-chr4_GL456216_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.36mers.mm10-chr4_GL456350_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.36mers.mm10-chr4_GL456350_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.36mers.mm10-chr4_JH584292_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.36mers.mm10-chr4_JH584292_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.36mers.mm10-chr4_JH584293_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.36mers.mm10-chr4_JH584293_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.36mers.mm10-chr4_JH584294_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.36mers.mm10-chr4_JH584294_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.36mers.mm10-chr4_JH584295_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.36mers.mm10-chr4_JH584295_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.36mers.mm10-chr5.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.36mers.mm10-chr5.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.36mers.mm10-chr5_GL456354_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.36mers.mm10-chr5_GL456354_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.36mers.mm10-chr5_JH584296_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.36mers.mm10-chr5_JH584296_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.36mers.mm10-chr5_JH584297_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.36mers.mm10-chr5_JH584297_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.36mers.mm10-chr5_JH584298_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.36mers.mm10-chr5_JH584298_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.36mers.mm10-chr5_JH584299_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.36mers.mm10-chr5_JH584299_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.36mers.mm10-chr6.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.36mers.mm10-chr6.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.36mers.mm10-chr7.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.36mers.mm10-chr7.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.36mers.mm10-chr7_GL456219_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.36mers.mm10-chr7_GL456219_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.36mers.mm10-chr8.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.36mers.mm10-chr8.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.36mers.mm10-chr9.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.36mers.mm10-chr9.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.36mers.mm10-chrM.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.36mers.mm10-chrM.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.36mers.mm10-chrUn_GL456239.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.36mers.mm10-chrUn_GL456239.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.36mers.mm10-chrUn_GL456359.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.36mers.mm10-chrUn_GL456359.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.36mers.mm10-chrUn_GL456360.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.36mers.mm10-chrUn_GL456360.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.36mers.mm10-chrUn_GL456366.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.36mers.mm10-chrUn_GL456366.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.36mers.mm10-chrUn_GL456367.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.36mers.mm10-chrUn_GL456367.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.36mers.mm10-chrUn_GL456368.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.36mers.mm10-chrUn_GL456368.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.36mers.mm10-chrUn_GL456370.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.36mers.mm10-chrUn_GL456370.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.36mers.mm10-chrUn_GL456372.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.36mers.mm10-chrUn_GL456372.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.36mers.mm10-chrUn_GL456378.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.36mers.mm10-chrUn_GL456378.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.36mers.mm10-chrUn_GL456379.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.36mers.mm10-chrUn_GL456379.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.36mers.mm10-chrUn_GL456381.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.36mers.mm10-chrUn_GL456381.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.36mers.mm10-chrUn_GL456382.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.36mers.mm10-chrUn_GL456382.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.36mers.mm10-chrUn_GL456383.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.36mers.mm10-chrUn_GL456383.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.36mers.mm10-chrUn_GL456385.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.36mers.mm10-chrUn_GL456385.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.36mers.mm10-chrUn_GL456387.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.36mers.mm10-chrUn_GL456387.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.36mers.mm10-chrUn_GL456389.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.36mers.mm10-chrUn_GL456389.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.36mers.mm10-chrUn_GL456390.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.36mers.mm10-chrUn_GL456390.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.36mers.mm10-chrUn_GL456392.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.36mers.mm10-chrUn_GL456392.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.36mers.mm10-chrUn_GL456393.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.36mers.mm10-chrUn_GL456393.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.36mers.mm10-chrUn_GL456394.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.36mers.mm10-chrUn_GL456394.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.36mers.mm10-chrUn_GL456396.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.36mers.mm10-chrUn_GL456396.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.36mers.mm10-chrUn_JH584304.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.36mers.mm10-chrUn_JH584304.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.36mers.mm10-chrX.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.36mers.mm10-chrX.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.36mers.mm10-chrX_GL456233_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.36mers.mm10-chrX_GL456233_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.36mers.mm10-chrY.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.36mers.mm10-chrY.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.36mers.mm10-chrY_JH584300_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.36mers.mm10-chrY_JH584300_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.36mers.mm10-chrY_JH584301_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.36mers.mm10-chrY_JH584301_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.36mers.mm10-chrY_JH584302_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.36mers.mm10-chrY_JH584302_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.36mers.mm10-chrY_JH584303_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.36mers.mm10-chrY_JH584303_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.50mers.hg38-chr10.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.50mers.hg38-chr10.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.50mers.hg38-chr11.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.50mers.hg38-chr11.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.50mers.hg38-chr11_KI270721v1_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.50mers.hg38-chr11_KI270721v1_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.50mers.hg38-chr12.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.50mers.hg38-chr12.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.50mers.hg38-chr13.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.50mers.hg38-chr13.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.50mers.hg38-chr14.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.50mers.hg38-chr14.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.50mers.hg38-chr14_GL000009v2_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.50mers.hg38-chr14_GL000009v2_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.50mers.hg38-chr14_GL000194v1_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.50mers.hg38-chr14_GL000194v1_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.50mers.hg38-chr14_GL000225v1_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.50mers.hg38-chr14_GL000225v1_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.50mers.hg38-chr14_KI270722v1_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.50mers.hg38-chr14_KI270722v1_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.50mers.hg38-chr14_KI270723v1_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.50mers.hg38-chr14_KI270723v1_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.50mers.hg38-chr14_KI270724v1_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.50mers.hg38-chr14_KI270724v1_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.50mers.hg38-chr14_KI270725v1_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.50mers.hg38-chr14_KI270725v1_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.50mers.hg38-chr14_KI270726v1_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.50mers.hg38-chr14_KI270726v1_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.50mers.hg38-chr15.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.50mers.hg38-chr15.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.50mers.hg38-chr15_KI270727v1_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.50mers.hg38-chr15_KI270727v1_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.50mers.hg38-chr16.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.50mers.hg38-chr16.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.50mers.hg38-chr16_KI270728v1_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.50mers.hg38-chr16_KI270728v1_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.50mers.hg38-chr17.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.50mers.hg38-chr17.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.50mers.hg38-chr17_GL000205v2_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.50mers.hg38-chr17_GL000205v2_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.50mers.hg38-chr17_KI270729v1_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.50mers.hg38-chr17_KI270729v1_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.50mers.hg38-chr17_KI270730v1_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.50mers.hg38-chr17_KI270730v1_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.50mers.hg38-chr18.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.50mers.hg38-chr18.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.50mers.hg38-chr19.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.50mers.hg38-chr19.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.50mers.hg38-chr1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.50mers.hg38-chr1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.50mers.hg38-chr1_KI270706v1_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.50mers.hg38-chr1_KI270706v1_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.50mers.hg38-chr1_KI270707v1_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.50mers.hg38-chr1_KI270707v1_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.50mers.hg38-chr1_KI270708v1_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.50mers.hg38-chr1_KI270708v1_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.50mers.hg38-chr1_KI270709v1_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.50mers.hg38-chr1_KI270709v1_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.50mers.hg38-chr1_KI270710v1_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.50mers.hg38-chr1_KI270710v1_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.50mers.hg38-chr1_KI270711v1_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.50mers.hg38-chr1_KI270711v1_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.50mers.hg38-chr1_KI270712v1_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.50mers.hg38-chr1_KI270712v1_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.50mers.hg38-chr1_KI270713v1_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.50mers.hg38-chr1_KI270713v1_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.50mers.hg38-chr1_KI270714v1_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.50mers.hg38-chr1_KI270714v1_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.50mers.hg38-chr20.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.50mers.hg38-chr20.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.50mers.hg38-chr21.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.50mers.hg38-chr21.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.50mers.hg38-chr22.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.50mers.hg38-chr22.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.50mers.hg38-chr22_KI270731v1_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.50mers.hg38-chr22_KI270731v1_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.50mers.hg38-chr22_KI270732v1_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.50mers.hg38-chr22_KI270732v1_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.50mers.hg38-chr22_KI270733v1_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.50mers.hg38-chr22_KI270733v1_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.50mers.hg38-chr22_KI270734v1_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.50mers.hg38-chr22_KI270734v1_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.50mers.hg38-chr22_KI270735v1_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.50mers.hg38-chr22_KI270735v1_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.50mers.hg38-chr22_KI270736v1_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.50mers.hg38-chr22_KI270736v1_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.50mers.hg38-chr22_KI270737v1_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.50mers.hg38-chr22_KI270737v1_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.50mers.hg38-chr22_KI270738v1_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.50mers.hg38-chr22_KI270738v1_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.50mers.hg38-chr22_KI270739v1_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.50mers.hg38-chr22_KI270739v1_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.50mers.hg38-chr2.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.50mers.hg38-chr2.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.50mers.hg38-chr2_KI270715v1_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.50mers.hg38-chr2_KI270715v1_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.50mers.hg38-chr2_KI270716v1_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.50mers.hg38-chr2_KI270716v1_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.50mers.hg38-chr3.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.50mers.hg38-chr3.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.50mers.hg38-chr3_GL000221v1_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.50mers.hg38-chr3_GL000221v1_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.50mers.hg38-chr4.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.50mers.hg38-chr4.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.50mers.hg38-chr4_GL000008v2_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.50mers.hg38-chr4_GL000008v2_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.50mers.hg38-chr5.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.50mers.hg38-chr5.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.50mers.hg38-chr5_GL000208v1_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.50mers.hg38-chr5_GL000208v1_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.50mers.hg38-chr6.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.50mers.hg38-chr6.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.50mers.hg38-chr7.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.50mers.hg38-chr7.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.50mers.hg38-chr8.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.50mers.hg38-chr8.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.50mers.hg38-chr9.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.50mers.hg38-chr9.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.50mers.hg38-chr9_KI270717v1_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.50mers.hg38-chr9_KI270717v1_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.50mers.hg38-chr9_KI270718v1_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.50mers.hg38-chr9_KI270718v1_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.50mers.hg38-chr9_KI270719v1_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.50mers.hg38-chr9_KI270719v1_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.50mers.hg38-chr9_KI270720v1_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.50mers.hg38-chr9_KI270720v1_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.50mers.hg38-chrM.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.50mers.hg38-chrM.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.50mers.hg38-chrUn_GL000195v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.50mers.hg38-chrUn_GL000195v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.50mers.hg38-chrUn_GL000213v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.50mers.hg38-chrUn_GL000213v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.50mers.hg38-chrUn_GL000214v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.50mers.hg38-chrUn_GL000214v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.50mers.hg38-chrUn_GL000216v2.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.50mers.hg38-chrUn_GL000216v2.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.50mers.hg38-chrUn_GL000218v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.50mers.hg38-chrUn_GL000218v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.50mers.hg38-chrUn_GL000219v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.50mers.hg38-chrUn_GL000219v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.50mers.hg38-chrUn_GL000220v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.50mers.hg38-chrUn_GL000220v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.50mers.hg38-chrUn_GL000224v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.50mers.hg38-chrUn_GL000224v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.50mers.hg38-chrUn_GL000226v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.50mers.hg38-chrUn_GL000226v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.50mers.hg38-chrUn_KI270302v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.50mers.hg38-chrUn_KI270302v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.50mers.hg38-chrUn_KI270303v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.50mers.hg38-chrUn_KI270303v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.50mers.hg38-chrUn_KI270304v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.50mers.hg38-chrUn_KI270304v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.50mers.hg38-chrUn_KI270305v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.50mers.hg38-chrUn_KI270305v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.50mers.hg38-chrUn_KI270310v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.50mers.hg38-chrUn_KI270310v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.50mers.hg38-chrUn_KI270311v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.50mers.hg38-chrUn_KI270311v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.50mers.hg38-chrUn_KI270312v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.50mers.hg38-chrUn_KI270312v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.50mers.hg38-chrUn_KI270315v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.50mers.hg38-chrUn_KI270315v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.50mers.hg38-chrUn_KI270316v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.50mers.hg38-chrUn_KI270316v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.50mers.hg38-chrUn_KI270317v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.50mers.hg38-chrUn_KI270317v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.50mers.hg38-chrUn_KI270320v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.50mers.hg38-chrUn_KI270320v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.50mers.hg38-chrUn_KI270322v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.50mers.hg38-chrUn_KI270322v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.50mers.hg38-chrUn_KI270329v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.50mers.hg38-chrUn_KI270329v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.50mers.hg38-chrUn_KI270330v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.50mers.hg38-chrUn_KI270330v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.50mers.hg38-chrUn_KI270333v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.50mers.hg38-chrUn_KI270333v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.50mers.hg38-chrUn_KI270334v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.50mers.hg38-chrUn_KI270334v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.50mers.hg38-chrUn_KI270335v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.50mers.hg38-chrUn_KI270335v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.50mers.hg38-chrUn_KI270336v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.50mers.hg38-chrUn_KI270336v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.50mers.hg38-chrUn_KI270337v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.50mers.hg38-chrUn_KI270337v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.50mers.hg38-chrUn_KI270338v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.50mers.hg38-chrUn_KI270338v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.50mers.hg38-chrUn_KI270340v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.50mers.hg38-chrUn_KI270340v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.50mers.hg38-chrUn_KI270362v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.50mers.hg38-chrUn_KI270362v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.50mers.hg38-chrUn_KI270363v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.50mers.hg38-chrUn_KI270363v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.50mers.hg38-chrUn_KI270364v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.50mers.hg38-chrUn_KI270364v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.50mers.hg38-chrUn_KI270366v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.50mers.hg38-chrUn_KI270366v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.50mers.hg38-chrUn_KI270371v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.50mers.hg38-chrUn_KI270371v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.50mers.hg38-chrUn_KI270372v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.50mers.hg38-chrUn_KI270372v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.50mers.hg38-chrUn_KI270373v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.50mers.hg38-chrUn_KI270373v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.50mers.hg38-chrUn_KI270374v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.50mers.hg38-chrUn_KI270374v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.50mers.hg38-chrUn_KI270375v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.50mers.hg38-chrUn_KI270375v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.50mers.hg38-chrUn_KI270376v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.50mers.hg38-chrUn_KI270376v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.50mers.hg38-chrUn_KI270378v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.50mers.hg38-chrUn_KI270378v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.50mers.hg38-chrUn_KI270379v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.50mers.hg38-chrUn_KI270379v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.50mers.hg38-chrUn_KI270381v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.50mers.hg38-chrUn_KI270381v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.50mers.hg38-chrUn_KI270382v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.50mers.hg38-chrUn_KI270382v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.50mers.hg38-chrUn_KI270383v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.50mers.hg38-chrUn_KI270383v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.50mers.hg38-chrUn_KI270384v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.50mers.hg38-chrUn_KI270384v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.50mers.hg38-chrUn_KI270385v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.50mers.hg38-chrUn_KI270385v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.50mers.hg38-chrUn_KI270386v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.50mers.hg38-chrUn_KI270386v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.50mers.hg38-chrUn_KI270387v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.50mers.hg38-chrUn_KI270387v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.50mers.hg38-chrUn_KI270388v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.50mers.hg38-chrUn_KI270388v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.50mers.hg38-chrUn_KI270389v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.50mers.hg38-chrUn_KI270389v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.50mers.hg38-chrUn_KI270390v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.50mers.hg38-chrUn_KI270390v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.50mers.hg38-chrUn_KI270391v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.50mers.hg38-chrUn_KI270391v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.50mers.hg38-chrUn_KI270392v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.50mers.hg38-chrUn_KI270392v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.50mers.hg38-chrUn_KI270393v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.50mers.hg38-chrUn_KI270393v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.50mers.hg38-chrUn_KI270394v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.50mers.hg38-chrUn_KI270394v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.50mers.hg38-chrUn_KI270395v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.50mers.hg38-chrUn_KI270395v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.50mers.hg38-chrUn_KI270396v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.50mers.hg38-chrUn_KI270396v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.50mers.hg38-chrUn_KI270411v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.50mers.hg38-chrUn_KI270411v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.50mers.hg38-chrUn_KI270412v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.50mers.hg38-chrUn_KI270412v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.50mers.hg38-chrUn_KI270414v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.50mers.hg38-chrUn_KI270414v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.50mers.hg38-chrUn_KI270417v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.50mers.hg38-chrUn_KI270417v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.50mers.hg38-chrUn_KI270418v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.50mers.hg38-chrUn_KI270418v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.50mers.hg38-chrUn_KI270419v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.50mers.hg38-chrUn_KI270419v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.50mers.hg38-chrUn_KI270420v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.50mers.hg38-chrUn_KI270420v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.50mers.hg38-chrUn_KI270422v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.50mers.hg38-chrUn_KI270422v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.50mers.hg38-chrUn_KI270423v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.50mers.hg38-chrUn_KI270423v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.50mers.hg38-chrUn_KI270424v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.50mers.hg38-chrUn_KI270424v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.50mers.hg38-chrUn_KI270425v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.50mers.hg38-chrUn_KI270425v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.50mers.hg38-chrUn_KI270429v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.50mers.hg38-chrUn_KI270429v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.50mers.hg38-chrUn_KI270435v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.50mers.hg38-chrUn_KI270435v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.50mers.hg38-chrUn_KI270438v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.50mers.hg38-chrUn_KI270438v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.50mers.hg38-chrUn_KI270442v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.50mers.hg38-chrUn_KI270442v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.50mers.hg38-chrUn_KI270448v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.50mers.hg38-chrUn_KI270448v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.50mers.hg38-chrUn_KI270465v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.50mers.hg38-chrUn_KI270465v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.50mers.hg38-chrUn_KI270466v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.50mers.hg38-chrUn_KI270466v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.50mers.hg38-chrUn_KI270467v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.50mers.hg38-chrUn_KI270467v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.50mers.hg38-chrUn_KI270468v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.50mers.hg38-chrUn_KI270468v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.50mers.hg38-chrUn_KI270507v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.50mers.hg38-chrUn_KI270507v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.50mers.hg38-chrUn_KI270508v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.50mers.hg38-chrUn_KI270508v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.50mers.hg38-chrUn_KI270509v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.50mers.hg38-chrUn_KI270509v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.50mers.hg38-chrUn_KI270510v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.50mers.hg38-chrUn_KI270510v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.50mers.hg38-chrUn_KI270511v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.50mers.hg38-chrUn_KI270511v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.50mers.hg38-chrUn_KI270512v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.50mers.hg38-chrUn_KI270512v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.50mers.hg38-chrUn_KI270515v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.50mers.hg38-chrUn_KI270515v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.50mers.hg38-chrUn_KI270516v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.50mers.hg38-chrUn_KI270516v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.50mers.hg38-chrUn_KI270517v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.50mers.hg38-chrUn_KI270517v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.50mers.hg38-chrUn_KI270518v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.50mers.hg38-chrUn_KI270518v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.50mers.hg38-chrUn_KI270519v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.50mers.hg38-chrUn_KI270519v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.50mers.hg38-chrUn_KI270521v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.50mers.hg38-chrUn_KI270521v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.50mers.hg38-chrUn_KI270522v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.50mers.hg38-chrUn_KI270522v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.50mers.hg38-chrUn_KI270528v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.50mers.hg38-chrUn_KI270528v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.50mers.hg38-chrUn_KI270529v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.50mers.hg38-chrUn_KI270529v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.50mers.hg38-chrUn_KI270530v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.50mers.hg38-chrUn_KI270530v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.50mers.hg38-chrUn_KI270538v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.50mers.hg38-chrUn_KI270538v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.50mers.hg38-chrUn_KI270539v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.50mers.hg38-chrUn_KI270539v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.50mers.hg38-chrUn_KI270544v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.50mers.hg38-chrUn_KI270544v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.50mers.hg38-chrUn_KI270548v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.50mers.hg38-chrUn_KI270548v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.50mers.hg38-chrUn_KI270579v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.50mers.hg38-chrUn_KI270579v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.50mers.hg38-chrUn_KI270580v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.50mers.hg38-chrUn_KI270580v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.50mers.hg38-chrUn_KI270581v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.50mers.hg38-chrUn_KI270581v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.50mers.hg38-chrUn_KI270582v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.50mers.hg38-chrUn_KI270582v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.50mers.hg38-chrUn_KI270583v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.50mers.hg38-chrUn_KI270583v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.50mers.hg38-chrUn_KI270584v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.50mers.hg38-chrUn_KI270584v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.50mers.hg38-chrUn_KI270587v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.50mers.hg38-chrUn_KI270587v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.50mers.hg38-chrUn_KI270588v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.50mers.hg38-chrUn_KI270588v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.50mers.hg38-chrUn_KI270589v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.50mers.hg38-chrUn_KI270589v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.50mers.hg38-chrUn_KI270590v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.50mers.hg38-chrUn_KI270590v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.50mers.hg38-chrUn_KI270591v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.50mers.hg38-chrUn_KI270591v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.50mers.hg38-chrUn_KI270593v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.50mers.hg38-chrUn_KI270593v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.50mers.hg38-chrUn_KI270741v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.50mers.hg38-chrUn_KI270741v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.50mers.hg38-chrUn_KI270742v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.50mers.hg38-chrUn_KI270742v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.50mers.hg38-chrUn_KI270743v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.50mers.hg38-chrUn_KI270743v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.50mers.hg38-chrUn_KI270744v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.50mers.hg38-chrUn_KI270744v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.50mers.hg38-chrUn_KI270745v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.50mers.hg38-chrUn_KI270745v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.50mers.hg38-chrUn_KI270746v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.50mers.hg38-chrUn_KI270746v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.50mers.hg38-chrUn_KI270747v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.50mers.hg38-chrUn_KI270747v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.50mers.hg38-chrUn_KI270748v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.50mers.hg38-chrUn_KI270748v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.50mers.hg38-chrUn_KI270749v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.50mers.hg38-chrUn_KI270749v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.50mers.hg38-chrUn_KI270750v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.50mers.hg38-chrUn_KI270750v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.50mers.hg38-chrUn_KI270751v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.50mers.hg38-chrUn_KI270751v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.50mers.hg38-chrUn_KI270752v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.50mers.hg38-chrUn_KI270752v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.50mers.hg38-chrUn_KI270753v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.50mers.hg38-chrUn_KI270753v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.50mers.hg38-chrUn_KI270754v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.50mers.hg38-chrUn_KI270754v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.50mers.hg38-chrUn_KI270755v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.50mers.hg38-chrUn_KI270755v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.50mers.hg38-chrUn_KI270756v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.50mers.hg38-chrUn_KI270756v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.50mers.hg38-chrUn_KI270757v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.50mers.hg38-chrUn_KI270757v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.50mers.hg38-chrX.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.50mers.hg38-chrX.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.50mers.hg38-chrY.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.50mers.hg38-chrY.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.50mers.hg38-chrY_KI270740v1_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.50mers.hg38-chrY_KI270740v1_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.50mers.mm10-chr10.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.50mers.mm10-chr10.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.50mers.mm10-chr11.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.50mers.mm10-chr11.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.50mers.mm10-chr12.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.50mers.mm10-chr12.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.50mers.mm10-chr13.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.50mers.mm10-chr13.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.50mers.mm10-chr14.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.50mers.mm10-chr14.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.50mers.mm10-chr15.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.50mers.mm10-chr15.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.50mers.mm10-chr16.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.50mers.mm10-chr16.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.50mers.mm10-chr17.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.50mers.mm10-chr17.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.50mers.mm10-chr18.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.50mers.mm10-chr18.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.50mers.mm10-chr19.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.50mers.mm10-chr19.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.50mers.mm10-chr1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.50mers.mm10-chr1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.50mers.mm10-chr1_GL456210_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.50mers.mm10-chr1_GL456210_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.50mers.mm10-chr1_GL456211_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.50mers.mm10-chr1_GL456211_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.50mers.mm10-chr1_GL456212_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.50mers.mm10-chr1_GL456212_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.50mers.mm10-chr1_GL456213_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.50mers.mm10-chr1_GL456213_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.50mers.mm10-chr1_GL456221_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.50mers.mm10-chr1_GL456221_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.50mers.mm10-chr2.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.50mers.mm10-chr2.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.50mers.mm10-chr3.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.50mers.mm10-chr3.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.50mers.mm10-chr4.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.50mers.mm10-chr4.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.50mers.mm10-chr4_GL456216_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.50mers.mm10-chr4_GL456216_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.50mers.mm10-chr4_GL456350_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.50mers.mm10-chr4_GL456350_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.50mers.mm10-chr4_JH584292_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.50mers.mm10-chr4_JH584292_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.50mers.mm10-chr4_JH584293_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.50mers.mm10-chr4_JH584293_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.50mers.mm10-chr4_JH584294_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.50mers.mm10-chr4_JH584294_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.50mers.mm10-chr4_JH584295_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.50mers.mm10-chr4_JH584295_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.50mers.mm10-chr5.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.50mers.mm10-chr5.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.50mers.mm10-chr5_GL456354_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.50mers.mm10-chr5_GL456354_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.50mers.mm10-chr5_JH584296_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.50mers.mm10-chr5_JH584296_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.50mers.mm10-chr5_JH584297_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.50mers.mm10-chr5_JH584297_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.50mers.mm10-chr5_JH584298_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.50mers.mm10-chr5_JH584298_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.50mers.mm10-chr5_JH584299_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.50mers.mm10-chr5_JH584299_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.50mers.mm10-chr6.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.50mers.mm10-chr6.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.50mers.mm10-chr7.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.50mers.mm10-chr7.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.50mers.mm10-chr7_GL456219_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.50mers.mm10-chr7_GL456219_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.50mers.mm10-chr8.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.50mers.mm10-chr8.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.50mers.mm10-chr9.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.50mers.mm10-chr9.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.50mers.mm10-chrM.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.50mers.mm10-chrM.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.50mers.mm10-chrUn_GL456239.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.50mers.mm10-chrUn_GL456239.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.50mers.mm10-chrUn_GL456359.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.50mers.mm10-chrUn_GL456359.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.50mers.mm10-chrUn_GL456360.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.50mers.mm10-chrUn_GL456360.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.50mers.mm10-chrUn_GL456366.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.50mers.mm10-chrUn_GL456366.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.50mers.mm10-chrUn_GL456367.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.50mers.mm10-chrUn_GL456367.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.50mers.mm10-chrUn_GL456368.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.50mers.mm10-chrUn_GL456368.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.50mers.mm10-chrUn_GL456370.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.50mers.mm10-chrUn_GL456370.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.50mers.mm10-chrUn_GL456372.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.50mers.mm10-chrUn_GL456372.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.50mers.mm10-chrUn_GL456378.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.50mers.mm10-chrUn_GL456378.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.50mers.mm10-chrUn_GL456379.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.50mers.mm10-chrUn_GL456379.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.50mers.mm10-chrUn_GL456381.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.50mers.mm10-chrUn_GL456381.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.50mers.mm10-chrUn_GL456382.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.50mers.mm10-chrUn_GL456382.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.50mers.mm10-chrUn_GL456383.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.50mers.mm10-chrUn_GL456383.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.50mers.mm10-chrUn_GL456385.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.50mers.mm10-chrUn_GL456385.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.50mers.mm10-chrUn_GL456387.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.50mers.mm10-chrUn_GL456387.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.50mers.mm10-chrUn_GL456389.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.50mers.mm10-chrUn_GL456389.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.50mers.mm10-chrUn_GL456390.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.50mers.mm10-chrUn_GL456390.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.50mers.mm10-chrUn_GL456392.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.50mers.mm10-chrUn_GL456392.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.50mers.mm10-chrUn_GL456393.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.50mers.mm10-chrUn_GL456393.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.50mers.mm10-chrUn_GL456394.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.50mers.mm10-chrUn_GL456394.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.50mers.mm10-chrUn_GL456396.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.50mers.mm10-chrUn_GL456396.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.50mers.mm10-chrUn_JH584304.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.50mers.mm10-chrUn_JH584304.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.50mers.mm10-chrX.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.50mers.mm10-chrX.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.50mers.mm10-chrX_GL456233_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.50mers.mm10-chrX_GL456233_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.50mers.mm10-chrY.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.50mers.mm10-chrY.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.50mers.mm10-chrY_JH584300_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.50mers.mm10-chrY_JH584300_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.50mers.mm10-chrY_JH584301_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.50mers.mm10-chrY_JH584301_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.50mers.mm10-chrY_JH584302_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.50mers.mm10-chrY_JH584302_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.50mers.mm10-chrY_JH584303_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.50mers.mm10-chrY_JH584303_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.75mers.hg38-chr10.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.75mers.hg38-chr10.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.75mers.hg38-chr11.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.75mers.hg38-chr11.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.75mers.hg38-chr11_KI270721v1_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.75mers.hg38-chr11_KI270721v1_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.75mers.hg38-chr12.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.75mers.hg38-chr12.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.75mers.hg38-chr13.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.75mers.hg38-chr13.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.75mers.hg38-chr14.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.75mers.hg38-chr14.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.75mers.hg38-chr14_GL000009v2_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.75mers.hg38-chr14_GL000009v2_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.75mers.hg38-chr14_GL000194v1_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.75mers.hg38-chr14_GL000194v1_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.75mers.hg38-chr14_GL000225v1_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.75mers.hg38-chr14_GL000225v1_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.75mers.hg38-chr14_KI270722v1_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.75mers.hg38-chr14_KI270722v1_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.75mers.hg38-chr14_KI270723v1_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.75mers.hg38-chr14_KI270723v1_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.75mers.hg38-chr14_KI270724v1_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.75mers.hg38-chr14_KI270724v1_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.75mers.hg38-chr14_KI270725v1_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.75mers.hg38-chr14_KI270725v1_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.75mers.hg38-chr14_KI270726v1_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.75mers.hg38-chr14_KI270726v1_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.75mers.hg38-chr15.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.75mers.hg38-chr15.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.75mers.hg38-chr15_KI270727v1_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.75mers.hg38-chr15_KI270727v1_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.75mers.hg38-chr16.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.75mers.hg38-chr16.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.75mers.hg38-chr16_KI270728v1_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.75mers.hg38-chr16_KI270728v1_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.75mers.hg38-chr17.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.75mers.hg38-chr17.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.75mers.hg38-chr17_GL000205v2_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.75mers.hg38-chr17_GL000205v2_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.75mers.hg38-chr17_KI270729v1_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.75mers.hg38-chr17_KI270729v1_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.75mers.hg38-chr17_KI270730v1_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.75mers.hg38-chr17_KI270730v1_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.75mers.hg38-chr18.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.75mers.hg38-chr18.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.75mers.hg38-chr19.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.75mers.hg38-chr19.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.75mers.hg38-chr1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.75mers.hg38-chr1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.75mers.hg38-chr1_KI270706v1_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.75mers.hg38-chr1_KI270706v1_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.75mers.hg38-chr1_KI270707v1_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.75mers.hg38-chr1_KI270707v1_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.75mers.hg38-chr1_KI270708v1_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.75mers.hg38-chr1_KI270708v1_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.75mers.hg38-chr1_KI270709v1_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.75mers.hg38-chr1_KI270709v1_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.75mers.hg38-chr1_KI270710v1_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.75mers.hg38-chr1_KI270710v1_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.75mers.hg38-chr1_KI270711v1_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.75mers.hg38-chr1_KI270711v1_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.75mers.hg38-chr1_KI270712v1_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.75mers.hg38-chr1_KI270712v1_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.75mers.hg38-chr1_KI270713v1_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.75mers.hg38-chr1_KI270713v1_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.75mers.hg38-chr1_KI270714v1_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.75mers.hg38-chr1_KI270714v1_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.75mers.hg38-chr20.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.75mers.hg38-chr20.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.75mers.hg38-chr21.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.75mers.hg38-chr21.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.75mers.hg38-chr22.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.75mers.hg38-chr22.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.75mers.hg38-chr22_KI270731v1_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.75mers.hg38-chr22_KI270731v1_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.75mers.hg38-chr22_KI270732v1_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.75mers.hg38-chr22_KI270732v1_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.75mers.hg38-chr22_KI270733v1_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.75mers.hg38-chr22_KI270733v1_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.75mers.hg38-chr22_KI270734v1_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.75mers.hg38-chr22_KI270734v1_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.75mers.hg38-chr22_KI270735v1_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.75mers.hg38-chr22_KI270735v1_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.75mers.hg38-chr22_KI270736v1_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.75mers.hg38-chr22_KI270736v1_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.75mers.hg38-chr22_KI270737v1_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.75mers.hg38-chr22_KI270737v1_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.75mers.hg38-chr22_KI270738v1_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.75mers.hg38-chr22_KI270738v1_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.75mers.hg38-chr22_KI270739v1_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.75mers.hg38-chr22_KI270739v1_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.75mers.hg38-chr2.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.75mers.hg38-chr2.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.75mers.hg38-chr2_KI270715v1_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.75mers.hg38-chr2_KI270715v1_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.75mers.hg38-chr2_KI270716v1_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.75mers.hg38-chr2_KI270716v1_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.75mers.hg38-chr3.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.75mers.hg38-chr3.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.75mers.hg38-chr3_GL000221v1_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.75mers.hg38-chr3_GL000221v1_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.75mers.hg38-chr4.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.75mers.hg38-chr4.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.75mers.hg38-chr4_GL000008v2_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.75mers.hg38-chr4_GL000008v2_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.75mers.hg38-chr5.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.75mers.hg38-chr5.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.75mers.hg38-chr5_GL000208v1_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.75mers.hg38-chr5_GL000208v1_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.75mers.hg38-chr6.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.75mers.hg38-chr6.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.75mers.hg38-chr7.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.75mers.hg38-chr7.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.75mers.hg38-chr8.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.75mers.hg38-chr8.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.75mers.hg38-chr9.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.75mers.hg38-chr9.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.75mers.hg38-chr9_KI270717v1_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.75mers.hg38-chr9_KI270717v1_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.75mers.hg38-chr9_KI270718v1_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.75mers.hg38-chr9_KI270718v1_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.75mers.hg38-chr9_KI270719v1_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.75mers.hg38-chr9_KI270719v1_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.75mers.hg38-chr9_KI270720v1_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.75mers.hg38-chr9_KI270720v1_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.75mers.hg38-chrM.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.75mers.hg38-chrM.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.75mers.hg38-chrUn_GL000195v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.75mers.hg38-chrUn_GL000195v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.75mers.hg38-chrUn_GL000213v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.75mers.hg38-chrUn_GL000213v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.75mers.hg38-chrUn_GL000214v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.75mers.hg38-chrUn_GL000214v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.75mers.hg38-chrUn_GL000216v2.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.75mers.hg38-chrUn_GL000216v2.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.75mers.hg38-chrUn_GL000218v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.75mers.hg38-chrUn_GL000218v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.75mers.hg38-chrUn_GL000219v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.75mers.hg38-chrUn_GL000219v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.75mers.hg38-chrUn_GL000220v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.75mers.hg38-chrUn_GL000220v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.75mers.hg38-chrUn_GL000224v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.75mers.hg38-chrUn_GL000224v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.75mers.hg38-chrUn_GL000226v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.75mers.hg38-chrUn_GL000226v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.75mers.hg38-chrUn_KI270302v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.75mers.hg38-chrUn_KI270302v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.75mers.hg38-chrUn_KI270303v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.75mers.hg38-chrUn_KI270303v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.75mers.hg38-chrUn_KI270304v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.75mers.hg38-chrUn_KI270304v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.75mers.hg38-chrUn_KI270305v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.75mers.hg38-chrUn_KI270305v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.75mers.hg38-chrUn_KI270310v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.75mers.hg38-chrUn_KI270310v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.75mers.hg38-chrUn_KI270311v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.75mers.hg38-chrUn_KI270311v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.75mers.hg38-chrUn_KI270312v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.75mers.hg38-chrUn_KI270312v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.75mers.hg38-chrUn_KI270315v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.75mers.hg38-chrUn_KI270315v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.75mers.hg38-chrUn_KI270316v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.75mers.hg38-chrUn_KI270316v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.75mers.hg38-chrUn_KI270317v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.75mers.hg38-chrUn_KI270317v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.75mers.hg38-chrUn_KI270320v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.75mers.hg38-chrUn_KI270320v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.75mers.hg38-chrUn_KI270322v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.75mers.hg38-chrUn_KI270322v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.75mers.hg38-chrUn_KI270329v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.75mers.hg38-chrUn_KI270329v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.75mers.hg38-chrUn_KI270330v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.75mers.hg38-chrUn_KI270330v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.75mers.hg38-chrUn_KI270333v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.75mers.hg38-chrUn_KI270333v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.75mers.hg38-chrUn_KI270334v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.75mers.hg38-chrUn_KI270334v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.75mers.hg38-chrUn_KI270335v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.75mers.hg38-chrUn_KI270335v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.75mers.hg38-chrUn_KI270336v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.75mers.hg38-chrUn_KI270336v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.75mers.hg38-chrUn_KI270337v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.75mers.hg38-chrUn_KI270337v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.75mers.hg38-chrUn_KI270338v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.75mers.hg38-chrUn_KI270338v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.75mers.hg38-chrUn_KI270340v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.75mers.hg38-chrUn_KI270340v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.75mers.hg38-chrUn_KI270362v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.75mers.hg38-chrUn_KI270362v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.75mers.hg38-chrUn_KI270363v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.75mers.hg38-chrUn_KI270363v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.75mers.hg38-chrUn_KI270364v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.75mers.hg38-chrUn_KI270364v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.75mers.hg38-chrUn_KI270366v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.75mers.hg38-chrUn_KI270366v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.75mers.hg38-chrUn_KI270371v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.75mers.hg38-chrUn_KI270371v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.75mers.hg38-chrUn_KI270372v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.75mers.hg38-chrUn_KI270372v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.75mers.hg38-chrUn_KI270373v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.75mers.hg38-chrUn_KI270373v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.75mers.hg38-chrUn_KI270374v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.75mers.hg38-chrUn_KI270374v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.75mers.hg38-chrUn_KI270375v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.75mers.hg38-chrUn_KI270375v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.75mers.hg38-chrUn_KI270376v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.75mers.hg38-chrUn_KI270376v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.75mers.hg38-chrUn_KI270378v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.75mers.hg38-chrUn_KI270378v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.75mers.hg38-chrUn_KI270379v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.75mers.hg38-chrUn_KI270379v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.75mers.hg38-chrUn_KI270381v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.75mers.hg38-chrUn_KI270381v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.75mers.hg38-chrUn_KI270382v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.75mers.hg38-chrUn_KI270382v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.75mers.hg38-chrUn_KI270383v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.75mers.hg38-chrUn_KI270383v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.75mers.hg38-chrUn_KI270384v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.75mers.hg38-chrUn_KI270384v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.75mers.hg38-chrUn_KI270385v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.75mers.hg38-chrUn_KI270385v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.75mers.hg38-chrUn_KI270386v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.75mers.hg38-chrUn_KI270386v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.75mers.hg38-chrUn_KI270387v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.75mers.hg38-chrUn_KI270387v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.75mers.hg38-chrUn_KI270388v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.75mers.hg38-chrUn_KI270388v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.75mers.hg38-chrUn_KI270389v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.75mers.hg38-chrUn_KI270389v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.75mers.hg38-chrUn_KI270390v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.75mers.hg38-chrUn_KI270390v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.75mers.hg38-chrUn_KI270391v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.75mers.hg38-chrUn_KI270391v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.75mers.hg38-chrUn_KI270392v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.75mers.hg38-chrUn_KI270392v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.75mers.hg38-chrUn_KI270393v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.75mers.hg38-chrUn_KI270393v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.75mers.hg38-chrUn_KI270394v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.75mers.hg38-chrUn_KI270394v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.75mers.hg38-chrUn_KI270395v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.75mers.hg38-chrUn_KI270395v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.75mers.hg38-chrUn_KI270396v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.75mers.hg38-chrUn_KI270396v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.75mers.hg38-chrUn_KI270411v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.75mers.hg38-chrUn_KI270411v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.75mers.hg38-chrUn_KI270412v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.75mers.hg38-chrUn_KI270412v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.75mers.hg38-chrUn_KI270414v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.75mers.hg38-chrUn_KI270414v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.75mers.hg38-chrUn_KI270417v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.75mers.hg38-chrUn_KI270417v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.75mers.hg38-chrUn_KI270418v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.75mers.hg38-chrUn_KI270418v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.75mers.hg38-chrUn_KI270419v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.75mers.hg38-chrUn_KI270419v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.75mers.hg38-chrUn_KI270420v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.75mers.hg38-chrUn_KI270420v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.75mers.hg38-chrUn_KI270422v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.75mers.hg38-chrUn_KI270422v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.75mers.hg38-chrUn_KI270423v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.75mers.hg38-chrUn_KI270423v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.75mers.hg38-chrUn_KI270424v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.75mers.hg38-chrUn_KI270424v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.75mers.hg38-chrUn_KI270425v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.75mers.hg38-chrUn_KI270425v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.75mers.hg38-chrUn_KI270429v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.75mers.hg38-chrUn_KI270429v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.75mers.hg38-chrUn_KI270435v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.75mers.hg38-chrUn_KI270435v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.75mers.hg38-chrUn_KI270438v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.75mers.hg38-chrUn_KI270438v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.75mers.hg38-chrUn_KI270442v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.75mers.hg38-chrUn_KI270442v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.75mers.hg38-chrUn_KI270448v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.75mers.hg38-chrUn_KI270448v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.75mers.hg38-chrUn_KI270465v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.75mers.hg38-chrUn_KI270465v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.75mers.hg38-chrUn_KI270466v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.75mers.hg38-chrUn_KI270466v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.75mers.hg38-chrUn_KI270467v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.75mers.hg38-chrUn_KI270467v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.75mers.hg38-chrUn_KI270468v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.75mers.hg38-chrUn_KI270468v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.75mers.hg38-chrUn_KI270507v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.75mers.hg38-chrUn_KI270507v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.75mers.hg38-chrUn_KI270508v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.75mers.hg38-chrUn_KI270508v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.75mers.hg38-chrUn_KI270509v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.75mers.hg38-chrUn_KI270509v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.75mers.hg38-chrUn_KI270510v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.75mers.hg38-chrUn_KI270510v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.75mers.hg38-chrUn_KI270511v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.75mers.hg38-chrUn_KI270511v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.75mers.hg38-chrUn_KI270512v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.75mers.hg38-chrUn_KI270512v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.75mers.hg38-chrUn_KI270515v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.75mers.hg38-chrUn_KI270515v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.75mers.hg38-chrUn_KI270516v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.75mers.hg38-chrUn_KI270516v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.75mers.hg38-chrUn_KI270517v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.75mers.hg38-chrUn_KI270517v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.75mers.hg38-chrUn_KI270518v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.75mers.hg38-chrUn_KI270518v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.75mers.hg38-chrUn_KI270519v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.75mers.hg38-chrUn_KI270519v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.75mers.hg38-chrUn_KI270521v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.75mers.hg38-chrUn_KI270521v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.75mers.hg38-chrUn_KI270522v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.75mers.hg38-chrUn_KI270522v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.75mers.hg38-chrUn_KI270528v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.75mers.hg38-chrUn_KI270528v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.75mers.hg38-chrUn_KI270529v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.75mers.hg38-chrUn_KI270529v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.75mers.hg38-chrUn_KI270530v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.75mers.hg38-chrUn_KI270530v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.75mers.hg38-chrUn_KI270538v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.75mers.hg38-chrUn_KI270538v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.75mers.hg38-chrUn_KI270539v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.75mers.hg38-chrUn_KI270539v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.75mers.hg38-chrUn_KI270544v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.75mers.hg38-chrUn_KI270544v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.75mers.hg38-chrUn_KI270548v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.75mers.hg38-chrUn_KI270548v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.75mers.hg38-chrUn_KI270579v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.75mers.hg38-chrUn_KI270579v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.75mers.hg38-chrUn_KI270580v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.75mers.hg38-chrUn_KI270580v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.75mers.hg38-chrUn_KI270581v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.75mers.hg38-chrUn_KI270581v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.75mers.hg38-chrUn_KI270582v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.75mers.hg38-chrUn_KI270582v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.75mers.hg38-chrUn_KI270583v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.75mers.hg38-chrUn_KI270583v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.75mers.hg38-chrUn_KI270584v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.75mers.hg38-chrUn_KI270584v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.75mers.hg38-chrUn_KI270587v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.75mers.hg38-chrUn_KI270587v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.75mers.hg38-chrUn_KI270588v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.75mers.hg38-chrUn_KI270588v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.75mers.hg38-chrUn_KI270589v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.75mers.hg38-chrUn_KI270589v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.75mers.hg38-chrUn_KI270590v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.75mers.hg38-chrUn_KI270590v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.75mers.hg38-chrUn_KI270591v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.75mers.hg38-chrUn_KI270591v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.75mers.hg38-chrUn_KI270593v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.75mers.hg38-chrUn_KI270593v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.75mers.hg38-chrUn_KI270741v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.75mers.hg38-chrUn_KI270741v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.75mers.hg38-chrUn_KI270742v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.75mers.hg38-chrUn_KI270742v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.75mers.hg38-chrUn_KI270743v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.75mers.hg38-chrUn_KI270743v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.75mers.hg38-chrUn_KI270744v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.75mers.hg38-chrUn_KI270744v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.75mers.hg38-chrUn_KI270745v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.75mers.hg38-chrUn_KI270745v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.75mers.hg38-chrUn_KI270746v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.75mers.hg38-chrUn_KI270746v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.75mers.hg38-chrUn_KI270747v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.75mers.hg38-chrUn_KI270747v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.75mers.hg38-chrUn_KI270748v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.75mers.hg38-chrUn_KI270748v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.75mers.hg38-chrUn_KI270749v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.75mers.hg38-chrUn_KI270749v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.75mers.hg38-chrUn_KI270750v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.75mers.hg38-chrUn_KI270750v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.75mers.hg38-chrUn_KI270751v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.75mers.hg38-chrUn_KI270751v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.75mers.hg38-chrUn_KI270752v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.75mers.hg38-chrUn_KI270752v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.75mers.hg38-chrUn_KI270753v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.75mers.hg38-chrUn_KI270753v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.75mers.hg38-chrUn_KI270754v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.75mers.hg38-chrUn_KI270754v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.75mers.hg38-chrUn_KI270755v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.75mers.hg38-chrUn_KI270755v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.75mers.hg38-chrUn_KI270756v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.75mers.hg38-chrUn_KI270756v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.75mers.hg38-chrUn_KI270757v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.75mers.hg38-chrUn_KI270757v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.75mers.hg38-chrX.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.75mers.hg38-chrX.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.75mers.hg38-chrY.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.75mers.hg38-chrY.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.75mers.hg38-chrY_KI270740v1_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.75mers.hg38-chrY_KI270740v1_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.75mers.mm10-chr10.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.75mers.mm10-chr10.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.75mers.mm10-chr11.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.75mers.mm10-chr11.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.75mers.mm10-chr12.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.75mers.mm10-chr12.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.75mers.mm10-chr13.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.75mers.mm10-chr13.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.75mers.mm10-chr14.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.75mers.mm10-chr14.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.75mers.mm10-chr15.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.75mers.mm10-chr15.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.75mers.mm10-chr16.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.75mers.mm10-chr16.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.75mers.mm10-chr17.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.75mers.mm10-chr17.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.75mers.mm10-chr18.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.75mers.mm10-chr18.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.75mers.mm10-chr19.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.75mers.mm10-chr19.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.75mers.mm10-chr1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.75mers.mm10-chr1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.75mers.mm10-chr1_GL456210_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.75mers.mm10-chr1_GL456210_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.75mers.mm10-chr1_GL456211_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.75mers.mm10-chr1_GL456211_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.75mers.mm10-chr1_GL456212_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.75mers.mm10-chr1_GL456212_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.75mers.mm10-chr1_GL456213_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.75mers.mm10-chr1_GL456213_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.75mers.mm10-chr1_GL456221_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.75mers.mm10-chr1_GL456221_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.75mers.mm10-chr2.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.75mers.mm10-chr2.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.75mers.mm10-chr3.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.75mers.mm10-chr3.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.75mers.mm10-chr4.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.75mers.mm10-chr4.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.75mers.mm10-chr4_GL456216_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.75mers.mm10-chr4_GL456216_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.75mers.mm10-chr4_GL456350_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.75mers.mm10-chr4_GL456350_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.75mers.mm10-chr4_JH584292_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.75mers.mm10-chr4_JH584292_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.75mers.mm10-chr4_JH584293_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.75mers.mm10-chr4_JH584293_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.75mers.mm10-chr4_JH584294_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.75mers.mm10-chr4_JH584294_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.75mers.mm10-chr4_JH584295_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.75mers.mm10-chr4_JH584295_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.75mers.mm10-chr5.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.75mers.mm10-chr5.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.75mers.mm10-chr5_GL456354_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.75mers.mm10-chr5_GL456354_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.75mers.mm10-chr5_JH584296_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.75mers.mm10-chr5_JH584296_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.75mers.mm10-chr5_JH584297_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.75mers.mm10-chr5_JH584297_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.75mers.mm10-chr5_JH584298_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.75mers.mm10-chr5_JH584298_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.75mers.mm10-chr5_JH584299_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.75mers.mm10-chr5_JH584299_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.75mers.mm10-chr6.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.75mers.mm10-chr6.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.75mers.mm10-chr7.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.75mers.mm10-chr7.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.75mers.mm10-chr7_GL456219_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.75mers.mm10-chr7_GL456219_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.75mers.mm10-chr8.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.75mers.mm10-chr8.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.75mers.mm10-chr9.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.75mers.mm10-chr9.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.75mers.mm10-chrM.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.75mers.mm10-chrM.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.75mers.mm10-chrUn_GL456239.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.75mers.mm10-chrUn_GL456239.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.75mers.mm10-chrUn_GL456359.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.75mers.mm10-chrUn_GL456359.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.75mers.mm10-chrUn_GL456360.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.75mers.mm10-chrUn_GL456360.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.75mers.mm10-chrUn_GL456366.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.75mers.mm10-chrUn_GL456366.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.75mers.mm10-chrUn_GL456367.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.75mers.mm10-chrUn_GL456367.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.75mers.mm10-chrUn_GL456368.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.75mers.mm10-chrUn_GL456368.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.75mers.mm10-chrUn_GL456370.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.75mers.mm10-chrUn_GL456370.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.75mers.mm10-chrUn_GL456372.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.75mers.mm10-chrUn_GL456372.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.75mers.mm10-chrUn_GL456378.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.75mers.mm10-chrUn_GL456378.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.75mers.mm10-chrUn_GL456379.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.75mers.mm10-chrUn_GL456379.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.75mers.mm10-chrUn_GL456381.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.75mers.mm10-chrUn_GL456381.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.75mers.mm10-chrUn_GL456382.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.75mers.mm10-chrUn_GL456382.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.75mers.mm10-chrUn_GL456383.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.75mers.mm10-chrUn_GL456383.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.75mers.mm10-chrUn_GL456385.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.75mers.mm10-chrUn_GL456385.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.75mers.mm10-chrUn_GL456387.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.75mers.mm10-chrUn_GL456387.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.75mers.mm10-chrUn_GL456389.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.75mers.mm10-chrUn_GL456389.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.75mers.mm10-chrUn_GL456390.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.75mers.mm10-chrUn_GL456390.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.75mers.mm10-chrUn_GL456392.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.75mers.mm10-chrUn_GL456392.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.75mers.mm10-chrUn_GL456393.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.75mers.mm10-chrUn_GL456393.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.75mers.mm10-chrUn_GL456394.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.75mers.mm10-chrUn_GL456394.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.75mers.mm10-chrUn_GL456396.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.75mers.mm10-chrUn_GL456396.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.75mers.mm10-chrUn_JH584304.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.75mers.mm10-chrUn_JH584304.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.75mers.mm10-chrX.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.75mers.mm10-chrX.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.75mers.mm10-chrX_GL456233_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.75mers.mm10-chrX_GL456233_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.75mers.mm10-chrY.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.75mers.mm10-chrY.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.75mers.mm10-chrY_JH584300_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.75mers.mm10-chrY_JH584300_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.75mers.mm10-chrY_JH584301_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.75mers.mm10-chrY_JH584301_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.75mers.mm10-chrY_JH584302_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.75mers.mm10-chrY_JH584302_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.75mers.mm10-chrY_JH584303_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.75mers.mm10-chrY_JH584303_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.100mers.hg38-chr10.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.100mers.hg38-chr10.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.100mers.hg38-chr11.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.100mers.hg38-chr11.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.100mers.hg38-chr11_KI270721v1_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.100mers.hg38-chr11_KI270721v1_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.100mers.hg38-chr12.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.100mers.hg38-chr12.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.100mers.hg38-chr13.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.100mers.hg38-chr13.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.100mers.hg38-chr14.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.100mers.hg38-chr14.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.100mers.hg38-chr14_GL000009v2_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.100mers.hg38-chr14_GL000009v2_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.100mers.hg38-chr14_GL000194v1_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.100mers.hg38-chr14_GL000194v1_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.100mers.hg38-chr14_GL000225v1_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.100mers.hg38-chr14_GL000225v1_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.100mers.hg38-chr14_KI270722v1_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.100mers.hg38-chr14_KI270722v1_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.100mers.hg38-chr14_KI270723v1_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.100mers.hg38-chr14_KI270723v1_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.100mers.hg38-chr14_KI270724v1_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.100mers.hg38-chr14_KI270724v1_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.100mers.hg38-chr14_KI270725v1_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.100mers.hg38-chr14_KI270725v1_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.100mers.hg38-chr14_KI270726v1_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.100mers.hg38-chr14_KI270726v1_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.100mers.hg38-chr15.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.100mers.hg38-chr15.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.100mers.hg38-chr15_KI270727v1_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.100mers.hg38-chr15_KI270727v1_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.100mers.hg38-chr16.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.100mers.hg38-chr16.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.100mers.hg38-chr16_KI270728v1_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.100mers.hg38-chr16_KI270728v1_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.100mers.hg38-chr17.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.100mers.hg38-chr17.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.100mers.hg38-chr17_GL000205v2_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.100mers.hg38-chr17_GL000205v2_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.100mers.hg38-chr17_KI270729v1_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.100mers.hg38-chr17_KI270729v1_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.100mers.hg38-chr17_KI270730v1_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.100mers.hg38-chr17_KI270730v1_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.100mers.hg38-chr18.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.100mers.hg38-chr18.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.100mers.hg38-chr19.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.100mers.hg38-chr19.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.100mers.hg38-chr1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.100mers.hg38-chr1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.100mers.hg38-chr1_KI270706v1_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.100mers.hg38-chr1_KI270706v1_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.100mers.hg38-chr1_KI270707v1_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.100mers.hg38-chr1_KI270707v1_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.100mers.hg38-chr1_KI270708v1_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.100mers.hg38-chr1_KI270708v1_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.100mers.hg38-chr1_KI270709v1_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.100mers.hg38-chr1_KI270709v1_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.100mers.hg38-chr1_KI270710v1_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.100mers.hg38-chr1_KI270710v1_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.100mers.hg38-chr1_KI270711v1_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.100mers.hg38-chr1_KI270711v1_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.100mers.hg38-chr1_KI270712v1_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.100mers.hg38-chr1_KI270712v1_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.100mers.hg38-chr1_KI270713v1_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.100mers.hg38-chr1_KI270713v1_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.100mers.hg38-chr1_KI270714v1_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.100mers.hg38-chr1_KI270714v1_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.100mers.hg38-chr20.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.100mers.hg38-chr20.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.100mers.hg38-chr21.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.100mers.hg38-chr21.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.100mers.hg38-chr22.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.100mers.hg38-chr22.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.100mers.hg38-chr22_KI270731v1_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.100mers.hg38-chr22_KI270731v1_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.100mers.hg38-chr22_KI270732v1_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.100mers.hg38-chr22_KI270732v1_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.100mers.hg38-chr22_KI270733v1_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.100mers.hg38-chr22_KI270733v1_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.100mers.hg38-chr22_KI270734v1_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.100mers.hg38-chr22_KI270734v1_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.100mers.hg38-chr22_KI270735v1_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.100mers.hg38-chr22_KI270735v1_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.100mers.hg38-chr22_KI270736v1_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.100mers.hg38-chr22_KI270736v1_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.100mers.hg38-chr22_KI270737v1_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.100mers.hg38-chr22_KI270737v1_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.100mers.hg38-chr22_KI270738v1_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.100mers.hg38-chr22_KI270738v1_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.100mers.hg38-chr22_KI270739v1_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.100mers.hg38-chr22_KI270739v1_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.100mers.hg38-chr2.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.100mers.hg38-chr2.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.100mers.hg38-chr2_KI270715v1_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.100mers.hg38-chr2_KI270715v1_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.100mers.hg38-chr2_KI270716v1_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.100mers.hg38-chr2_KI270716v1_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.100mers.hg38-chr3.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.100mers.hg38-chr3.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.100mers.hg38-chr3_GL000221v1_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.100mers.hg38-chr3_GL000221v1_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.100mers.hg38-chr4.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.100mers.hg38-chr4.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.100mers.hg38-chr4_GL000008v2_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.100mers.hg38-chr4_GL000008v2_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.100mers.hg38-chr5.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.100mers.hg38-chr5.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.100mers.hg38-chr5_GL000208v1_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.100mers.hg38-chr5_GL000208v1_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.100mers.hg38-chr6.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.100mers.hg38-chr6.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.100mers.hg38-chr7.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.100mers.hg38-chr7.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.100mers.hg38-chr8.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.100mers.hg38-chr8.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.100mers.hg38-chr9.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.100mers.hg38-chr9.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.100mers.hg38-chr9_KI270717v1_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.100mers.hg38-chr9_KI270717v1_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.100mers.hg38-chr9_KI270718v1_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.100mers.hg38-chr9_KI270718v1_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.100mers.hg38-chr9_KI270719v1_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.100mers.hg38-chr9_KI270719v1_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.100mers.hg38-chr9_KI270720v1_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.100mers.hg38-chr9_KI270720v1_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.100mers.hg38-chrM.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.100mers.hg38-chrM.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.100mers.hg38-chrUn_GL000195v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.100mers.hg38-chrUn_GL000195v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.100mers.hg38-chrUn_GL000213v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.100mers.hg38-chrUn_GL000213v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.100mers.hg38-chrUn_GL000214v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.100mers.hg38-chrUn_GL000214v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.100mers.hg38-chrUn_GL000216v2.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.100mers.hg38-chrUn_GL000216v2.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.100mers.hg38-chrUn_GL000218v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.100mers.hg38-chrUn_GL000218v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.100mers.hg38-chrUn_GL000219v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.100mers.hg38-chrUn_GL000219v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.100mers.hg38-chrUn_GL000220v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.100mers.hg38-chrUn_GL000220v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.100mers.hg38-chrUn_GL000224v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.100mers.hg38-chrUn_GL000224v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.100mers.hg38-chrUn_GL000226v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.100mers.hg38-chrUn_GL000226v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.100mers.hg38-chrUn_KI270302v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.100mers.hg38-chrUn_KI270302v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.100mers.hg38-chrUn_KI270303v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.100mers.hg38-chrUn_KI270303v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.100mers.hg38-chrUn_KI270304v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.100mers.hg38-chrUn_KI270304v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.100mers.hg38-chrUn_KI270305v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.100mers.hg38-chrUn_KI270305v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.100mers.hg38-chrUn_KI270310v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.100mers.hg38-chrUn_KI270310v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.100mers.hg38-chrUn_KI270311v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.100mers.hg38-chrUn_KI270311v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.100mers.hg38-chrUn_KI270312v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.100mers.hg38-chrUn_KI270312v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.100mers.hg38-chrUn_KI270315v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.100mers.hg38-chrUn_KI270315v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.100mers.hg38-chrUn_KI270316v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.100mers.hg38-chrUn_KI270316v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.100mers.hg38-chrUn_KI270317v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.100mers.hg38-chrUn_KI270317v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.100mers.hg38-chrUn_KI270320v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.100mers.hg38-chrUn_KI270320v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.100mers.hg38-chrUn_KI270322v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.100mers.hg38-chrUn_KI270322v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.100mers.hg38-chrUn_KI270329v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.100mers.hg38-chrUn_KI270329v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.100mers.hg38-chrUn_KI270330v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.100mers.hg38-chrUn_KI270330v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.100mers.hg38-chrUn_KI270333v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.100mers.hg38-chrUn_KI270333v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.100mers.hg38-chrUn_KI270334v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.100mers.hg38-chrUn_KI270334v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.100mers.hg38-chrUn_KI270335v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.100mers.hg38-chrUn_KI270335v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.100mers.hg38-chrUn_KI270336v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.100mers.hg38-chrUn_KI270336v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.100mers.hg38-chrUn_KI270337v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.100mers.hg38-chrUn_KI270337v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.100mers.hg38-chrUn_KI270338v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.100mers.hg38-chrUn_KI270338v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.100mers.hg38-chrUn_KI270340v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.100mers.hg38-chrUn_KI270340v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.100mers.hg38-chrUn_KI270362v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.100mers.hg38-chrUn_KI270362v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.100mers.hg38-chrUn_KI270363v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.100mers.hg38-chrUn_KI270363v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.100mers.hg38-chrUn_KI270364v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.100mers.hg38-chrUn_KI270364v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.100mers.hg38-chrUn_KI270366v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.100mers.hg38-chrUn_KI270366v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.100mers.hg38-chrUn_KI270371v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.100mers.hg38-chrUn_KI270371v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.100mers.hg38-chrUn_KI270372v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.100mers.hg38-chrUn_KI270372v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.100mers.hg38-chrUn_KI270373v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.100mers.hg38-chrUn_KI270373v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.100mers.hg38-chrUn_KI270374v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.100mers.hg38-chrUn_KI270374v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.100mers.hg38-chrUn_KI270375v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.100mers.hg38-chrUn_KI270375v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.100mers.hg38-chrUn_KI270376v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.100mers.hg38-chrUn_KI270376v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.100mers.hg38-chrUn_KI270378v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.100mers.hg38-chrUn_KI270378v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.100mers.hg38-chrUn_KI270379v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.100mers.hg38-chrUn_KI270379v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.100mers.hg38-chrUn_KI270381v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.100mers.hg38-chrUn_KI270381v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.100mers.hg38-chrUn_KI270382v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.100mers.hg38-chrUn_KI270382v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.100mers.hg38-chrUn_KI270383v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.100mers.hg38-chrUn_KI270383v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.100mers.hg38-chrUn_KI270384v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.100mers.hg38-chrUn_KI270384v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.100mers.hg38-chrUn_KI270385v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.100mers.hg38-chrUn_KI270385v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.100mers.hg38-chrUn_KI270386v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.100mers.hg38-chrUn_KI270386v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.100mers.hg38-chrUn_KI270387v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.100mers.hg38-chrUn_KI270387v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.100mers.hg38-chrUn_KI270388v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.100mers.hg38-chrUn_KI270388v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.100mers.hg38-chrUn_KI270389v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.100mers.hg38-chrUn_KI270389v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.100mers.hg38-chrUn_KI270390v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.100mers.hg38-chrUn_KI270390v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.100mers.hg38-chrUn_KI270391v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.100mers.hg38-chrUn_KI270391v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.100mers.hg38-chrUn_KI270392v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.100mers.hg38-chrUn_KI270392v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.100mers.hg38-chrUn_KI270393v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.100mers.hg38-chrUn_KI270393v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.100mers.hg38-chrUn_KI270394v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.100mers.hg38-chrUn_KI270394v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.100mers.hg38-chrUn_KI270395v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.100mers.hg38-chrUn_KI270395v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.100mers.hg38-chrUn_KI270396v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.100mers.hg38-chrUn_KI270396v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.100mers.hg38-chrUn_KI270411v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.100mers.hg38-chrUn_KI270411v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.100mers.hg38-chrUn_KI270412v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.100mers.hg38-chrUn_KI270412v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.100mers.hg38-chrUn_KI270414v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.100mers.hg38-chrUn_KI270414v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.100mers.hg38-chrUn_KI270417v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.100mers.hg38-chrUn_KI270417v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.100mers.hg38-chrUn_KI270418v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.100mers.hg38-chrUn_KI270418v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.100mers.hg38-chrUn_KI270419v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.100mers.hg38-chrUn_KI270419v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.100mers.hg38-chrUn_KI270420v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.100mers.hg38-chrUn_KI270420v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.100mers.hg38-chrUn_KI270422v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.100mers.hg38-chrUn_KI270422v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.100mers.hg38-chrUn_KI270423v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.100mers.hg38-chrUn_KI270423v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.100mers.hg38-chrUn_KI270424v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.100mers.hg38-chrUn_KI270424v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.100mers.hg38-chrUn_KI270425v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.100mers.hg38-chrUn_KI270425v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.100mers.hg38-chrUn_KI270429v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.100mers.hg38-chrUn_KI270429v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.100mers.hg38-chrUn_KI270435v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.100mers.hg38-chrUn_KI270435v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.100mers.hg38-chrUn_KI270438v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.100mers.hg38-chrUn_KI270438v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.100mers.hg38-chrUn_KI270442v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.100mers.hg38-chrUn_KI270442v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.100mers.hg38-chrUn_KI270448v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.100mers.hg38-chrUn_KI270448v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.100mers.hg38-chrUn_KI270465v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.100mers.hg38-chrUn_KI270465v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.100mers.hg38-chrUn_KI270466v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.100mers.hg38-chrUn_KI270466v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.100mers.hg38-chrUn_KI270467v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.100mers.hg38-chrUn_KI270467v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.100mers.hg38-chrUn_KI270468v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.100mers.hg38-chrUn_KI270468v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.100mers.hg38-chrUn_KI270507v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.100mers.hg38-chrUn_KI270507v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.100mers.hg38-chrUn_KI270508v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.100mers.hg38-chrUn_KI270508v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.100mers.hg38-chrUn_KI270509v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.100mers.hg38-chrUn_KI270509v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.100mers.hg38-chrUn_KI270510v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.100mers.hg38-chrUn_KI270510v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.100mers.hg38-chrUn_KI270511v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.100mers.hg38-chrUn_KI270511v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.100mers.hg38-chrUn_KI270512v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.100mers.hg38-chrUn_KI270512v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.100mers.hg38-chrUn_KI270515v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.100mers.hg38-chrUn_KI270515v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.100mers.hg38-chrUn_KI270516v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.100mers.hg38-chrUn_KI270516v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.100mers.hg38-chrUn_KI270517v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.100mers.hg38-chrUn_KI270517v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.100mers.hg38-chrUn_KI270518v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.100mers.hg38-chrUn_KI270518v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.100mers.hg38-chrUn_KI270519v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.100mers.hg38-chrUn_KI270519v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.100mers.hg38-chrUn_KI270521v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.100mers.hg38-chrUn_KI270521v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.100mers.hg38-chrUn_KI270522v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.100mers.hg38-chrUn_KI270522v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.100mers.hg38-chrUn_KI270528v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.100mers.hg38-chrUn_KI270528v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.100mers.hg38-chrUn_KI270529v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.100mers.hg38-chrUn_KI270529v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.100mers.hg38-chrUn_KI270530v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.100mers.hg38-chrUn_KI270530v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.100mers.hg38-chrUn_KI270538v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.100mers.hg38-chrUn_KI270538v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.100mers.hg38-chrUn_KI270539v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.100mers.hg38-chrUn_KI270539v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.100mers.hg38-chrUn_KI270544v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.100mers.hg38-chrUn_KI270544v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.100mers.hg38-chrUn_KI270548v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.100mers.hg38-chrUn_KI270548v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.100mers.hg38-chrUn_KI270579v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.100mers.hg38-chrUn_KI270579v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.100mers.hg38-chrUn_KI270580v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.100mers.hg38-chrUn_KI270580v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.100mers.hg38-chrUn_KI270581v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.100mers.hg38-chrUn_KI270581v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.100mers.hg38-chrUn_KI270582v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.100mers.hg38-chrUn_KI270582v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.100mers.hg38-chrUn_KI270583v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.100mers.hg38-chrUn_KI270583v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.100mers.hg38-chrUn_KI270584v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.100mers.hg38-chrUn_KI270584v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.100mers.hg38-chrUn_KI270587v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.100mers.hg38-chrUn_KI270587v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.100mers.hg38-chrUn_KI270588v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.100mers.hg38-chrUn_KI270588v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.100mers.hg38-chrUn_KI270589v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.100mers.hg38-chrUn_KI270589v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.100mers.hg38-chrUn_KI270590v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.100mers.hg38-chrUn_KI270590v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.100mers.hg38-chrUn_KI270591v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.100mers.hg38-chrUn_KI270591v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.100mers.hg38-chrUn_KI270593v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.100mers.hg38-chrUn_KI270593v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.100mers.hg38-chrUn_KI270741v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.100mers.hg38-chrUn_KI270741v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.100mers.hg38-chrUn_KI270742v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.100mers.hg38-chrUn_KI270742v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.100mers.hg38-chrUn_KI270743v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.100mers.hg38-chrUn_KI270743v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.100mers.hg38-chrUn_KI270744v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.100mers.hg38-chrUn_KI270744v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.100mers.hg38-chrUn_KI270745v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.100mers.hg38-chrUn_KI270745v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.100mers.hg38-chrUn_KI270746v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.100mers.hg38-chrUn_KI270746v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.100mers.hg38-chrUn_KI270747v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.100mers.hg38-chrUn_KI270747v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.100mers.hg38-chrUn_KI270748v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.100mers.hg38-chrUn_KI270748v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.100mers.hg38-chrUn_KI270749v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.100mers.hg38-chrUn_KI270749v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.100mers.hg38-chrUn_KI270750v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.100mers.hg38-chrUn_KI270750v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.100mers.hg38-chrUn_KI270751v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.100mers.hg38-chrUn_KI270751v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.100mers.hg38-chrUn_KI270752v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.100mers.hg38-chrUn_KI270752v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.100mers.hg38-chrUn_KI270753v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.100mers.hg38-chrUn_KI270753v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.100mers.hg38-chrUn_KI270754v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.100mers.hg38-chrUn_KI270754v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.100mers.hg38-chrUn_KI270755v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.100mers.hg38-chrUn_KI270755v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.100mers.hg38-chrUn_KI270756v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.100mers.hg38-chrUn_KI270756v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.100mers.hg38-chrUn_KI270757v1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.100mers.hg38-chrUn_KI270757v1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.100mers.hg38-chrX.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.100mers.hg38-chrX.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.100mers.hg38-chrY.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.100mers.hg38-chrY.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.100mers.hg38-chrY_KI270740v1_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.100mers.hg38-chrY_KI270740v1_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.100mers.mm10-chr10.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.100mers.mm10-chr10.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.100mers.mm10-chr11.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.100mers.mm10-chr11.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.100mers.mm10-chr12.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.100mers.mm10-chr12.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.100mers.mm10-chr13.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.100mers.mm10-chr13.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.100mers.mm10-chr14.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.100mers.mm10-chr14.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.100mers.mm10-chr15.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.100mers.mm10-chr15.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.100mers.mm10-chr16.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.100mers.mm10-chr16.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.100mers.mm10-chr17.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.100mers.mm10-chr17.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.100mers.mm10-chr18.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.100mers.mm10-chr18.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.100mers.mm10-chr19.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.100mers.mm10-chr19.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.100mers.mm10-chr1.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.100mers.mm10-chr1.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.100mers.mm10-chr1_GL456210_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.100mers.mm10-chr1_GL456210_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.100mers.mm10-chr1_GL456211_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.100mers.mm10-chr1_GL456211_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.100mers.mm10-chr1_GL456212_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.100mers.mm10-chr1_GL456212_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.100mers.mm10-chr1_GL456213_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.100mers.mm10-chr1_GL456213_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.100mers.mm10-chr1_GL456221_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.100mers.mm10-chr1_GL456221_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.100mers.mm10-chr2.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.100mers.mm10-chr2.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.100mers.mm10-chr3.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.100mers.mm10-chr3.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.100mers.mm10-chr4.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.100mers.mm10-chr4.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.100mers.mm10-chr4_GL456216_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.100mers.mm10-chr4_GL456216_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.100mers.mm10-chr4_GL456350_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.100mers.mm10-chr4_GL456350_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.100mers.mm10-chr4_JH584292_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.100mers.mm10-chr4_JH584292_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.100mers.mm10-chr4_JH584293_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.100mers.mm10-chr4_JH584293_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.100mers.mm10-chr4_JH584294_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.100mers.mm10-chr4_JH584294_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.100mers.mm10-chr4_JH584295_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.100mers.mm10-chr4_JH584295_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.100mers.mm10-chr5.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.100mers.mm10-chr5.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.100mers.mm10-chr5_GL456354_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.100mers.mm10-chr5_GL456354_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.100mers.mm10-chr5_JH584296_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.100mers.mm10-chr5_JH584296_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.100mers.mm10-chr5_JH584297_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.100mers.mm10-chr5_JH584297_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.100mers.mm10-chr5_JH584298_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.100mers.mm10-chr5_JH584298_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.100mers.mm10-chr5_JH584299_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.100mers.mm10-chr5_JH584299_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.100mers.mm10-chr6.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.100mers.mm10-chr6.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.100mers.mm10-chr7.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.100mers.mm10-chr7.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.100mers.mm10-chr7_GL456219_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.100mers.mm10-chr7_GL456219_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.100mers.mm10-chr8.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.100mers.mm10-chr8.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.100mers.mm10-chr9.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.100mers.mm10-chr9.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.100mers.mm10-chrM.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.100mers.mm10-chrM.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.100mers.mm10-chrUn_GL456239.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.100mers.mm10-chrUn_GL456239.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.100mers.mm10-chrUn_GL456359.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.100mers.mm10-chrUn_GL456359.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.100mers.mm10-chrUn_GL456360.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.100mers.mm10-chrUn_GL456360.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.100mers.mm10-chrUn_GL456366.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.100mers.mm10-chrUn_GL456366.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.100mers.mm10-chrUn_GL456367.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.100mers.mm10-chrUn_GL456367.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.100mers.mm10-chrUn_GL456368.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.100mers.mm10-chrUn_GL456368.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.100mers.mm10-chrUn_GL456370.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.100mers.mm10-chrUn_GL456370.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.100mers.mm10-chrUn_GL456372.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.100mers.mm10-chrUn_GL456372.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.100mers.mm10-chrUn_GL456378.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.100mers.mm10-chrUn_GL456378.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.100mers.mm10-chrUn_GL456379.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.100mers.mm10-chrUn_GL456379.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.100mers.mm10-chrUn_GL456381.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.100mers.mm10-chrUn_GL456381.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.100mers.mm10-chrUn_GL456382.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.100mers.mm10-chrUn_GL456382.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.100mers.mm10-chrUn_GL456383.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.100mers.mm10-chrUn_GL456383.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.100mers.mm10-chrUn_GL456385.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.100mers.mm10-chrUn_GL456385.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.100mers.mm10-chrUn_GL456387.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.100mers.mm10-chrUn_GL456387.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.100mers.mm10-chrUn_GL456389.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.100mers.mm10-chrUn_GL456389.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.100mers.mm10-chrUn_GL456390.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.100mers.mm10-chrUn_GL456390.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.100mers.mm10-chrUn_GL456392.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.100mers.mm10-chrUn_GL456392.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.100mers.mm10-chrUn_GL456393.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.100mers.mm10-chrUn_GL456393.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.100mers.mm10-chrUn_GL456394.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.100mers.mm10-chrUn_GL456394.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.100mers.mm10-chrUn_GL456396.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.100mers.mm10-chrUn_GL456396.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.100mers.mm10-chrUn_JH584304.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.100mers.mm10-chrUn_JH584304.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.100mers.mm10-chrX.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.100mers.mm10-chrX.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.100mers.mm10-chrX_GL456233_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.100mers.mm10-chrX_GL456233_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.100mers.mm10-chrY.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.100mers.mm10-chrY.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.100mers.mm10-chrY_JH584300_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.100mers.mm10-chrY_JH584300_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.100mers.mm10-chrY_JH584301_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.100mers.mm10-chrY_JH584301_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.100mers.mm10-chrY_JH584302_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.100mers.mm10-chrY_JH584302_random.hg38+mm10.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa hg38+mm10.100mers.mm10-chrY_JH584303_random.fa | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/bwa-indexes/hg38+mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - hg38+mm10.100mers.mm10-chrY_JH584303_random.hg38+mm10.unique