/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.17/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bwa-indexes/hg38-no-haps.fa L418D6D10ATACCL01.barcodes_annotated.UMI.gz_trimmed.revcomp_trimmed.revcomp.fq.gz | egrep -v chrM | ~/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bwa-indexes/hg38-no-haps.fa - | ~/programs/samtools-0.1.18/samtools sort - L418D6D10ATACCL01.trimmed.hg38.BWA.unique.nochrM
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.17/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bwa-indexes/hg38-no-haps.fa L420D6D10ATACCL03.barcodes_annotated.UMI.gz_trimmed.revcomp_trimmed.revcomp.fq.gz | egrep -v chrM | ~/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bwa-indexes/hg38-no-haps.fa - | ~/programs/samtools-0.1.18/samtools sort - L420D6D10ATACCL03.trimmed.hg38.BWA.unique.nochrM
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.17/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bwa-indexes/hg38-no-haps.fa L430D6D10ATACCL09.barcodes_annotated.UMI.gz_trimmed.revcomp_trimmed.revcomp.fq.gz | egrep -v chrM | ~/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bwa-indexes/hg38-no-haps.fa - | ~/programs/samtools-0.1.18/samtools sort - L430D6D10ATACCL09.trimmed.hg38.BWA.unique.nochrM
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.17/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bwa-indexes/hg38-no-haps.fa L431D6D10ATACCL10.barcodes_annotated.UMI.gz_trimmed.revcomp_trimmed.revcomp.fq.gz | egrep -v chrM | ~/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bwa-indexes/hg38-no-haps.fa - | ~/programs/samtools-0.1.18/samtools sort - L431D6D10ATACCL10.trimmed.hg38.BWA.unique.nochrM
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.17/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bwa-indexes/hg38-no-haps.fa L434D6D10ATACCL13.barcodes_annotated.UMI.gz_trimmed.revcomp_trimmed.revcomp.fq.gz | egrep -v chrM | ~/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bwa-indexes/hg38-no-haps.fa - | ~/programs/samtools-0.1.18/samtools sort - L434D6D10ATACCL13.trimmed.hg38.BWA.unique.nochrM
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.17/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bwa-indexes/hg38-no-haps.fa L435D6D10ATACCL14.barcodes_annotated.UMI.gz_trimmed.revcomp_trimmed.revcomp.fq.gz | egrep -v chrM | ~/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bwa-indexes/hg38-no-haps.fa - | ~/programs/samtools-0.1.18/samtools sort - L435D6D10ATACCL14.trimmed.hg38.BWA.unique.nochrM