bwa mem -t 8 -M ~/genomes/hg19/bwa-indexes/hg19-female.fa A-13189-1.end1_val_1.fq.gz A-13189-1.end2_val_2.fq.gz | ~/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT ~/genomes/hg19/sequence/hg19.fa - | ~/programs/samtools-0.1.18/samtools sort - A-13189-1.2x75mers-trimmed.bwa-mem.hg19-female
bwa mem -t 8 -M ~/genomes/hg19/bwa-indexes/hg19-female.fa A-13189-2.end1_val_1.fq.gz A-13189-2.end2_val_2.fq.gz | ~/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT ~/genomes/hg19/sequence/hg19.fa - | ~/programs/samtools-0.1.18/samtools sort - A-13189-2.2x75mers-trimmed.bwa-mem.hg19-female
bwa mem -t 8 -M ~/genomes/hg19/bwa-indexes/hg19-female.fa A-13190-1.end1_val_1.fq.gz A-13190-1.end2_val_2.fq.gz | ~/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT ~/genomes/hg19/sequence/hg19.fa - | ~/programs/samtools-0.1.18/samtools sort - A-13190-1.2x75mers-trimmed.bwa-mem.hg19-female
bwa mem -t 8 -M ~/genomes/hg19/bwa-indexes/hg19-female.fa A-13190-2.end1_val_1.fq.gz A-13190-2.end2_val_2.fq.gz | ~/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT ~/genomes/hg19/sequence/hg19.fa - | ~/programs/samtools-0.1.18/samtools sort - A-13190-2.2x75mers-trimmed.bwa-mem.hg19-female
bwa mem -t 8 -M ~/genomes/hg19/bwa-indexes/hg19-female.fa A-15171-1.end1_val_1.fq.gz A-15171-1.end2_val_2.fq.gz | ~/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT ~/genomes/hg19/sequence/hg19.fa - | ~/programs/samtools-0.1.18/samtools sort - A-15171-1.2x75mers-trimmed.bwa-mem.hg19-female
bwa mem -t 8 -M ~/genomes/hg19/bwa-indexes/hg19-female.fa A-15171-2.end1_val_1.fq.gz A-15171-2.end2_val_2.fq.gz | ~/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT ~/genomes/hg19/sequence/hg19.fa - | ~/programs/samtools-0.1.18/samtools sort - A-15171-2.2x75mers-trimmed.bwa-mem.hg19-female
bwa mem -t 8 -M ~/genomes/hg19/bwa-indexes/hg19-female.fa A-15173-1.end1_val_1.fq.gz A-15173-1.end2_val_2.fq.gz | ~/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT ~/genomes/hg19/sequence/hg19.fa - | ~/programs/samtools-0.1.18/samtools sort - A-15173-1.2x75mers-trimmed.bwa-mem.hg19-female
bwa mem -t 8 -M ~/genomes/hg19/bwa-indexes/hg19-female.fa A-15173-2.end1_val_1.fq.gz A-15173-2.end2_val_2.fq.gz | ~/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT ~/genomes/hg19/sequence/hg19.fa - | ~/programs/samtools-0.1.18/samtools sort - A-15173-2.2x75mers-trimmed.bwa-mem.hg19-female
bwa mem -t 8 -M ~/genomes/hg19/bwa-indexes/hg19-female.fa A-N4293-1.end1_val_1.fq.gz A-N4293-1.end2_val_2.fq.gz | ~/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT ~/genomes/hg19/sequence/hg19.fa - | ~/programs/samtools-0.1.18/samtools sort - A-N4293-1.2x75mers-trimmed.bwa-mem.hg19-female
bwa mem -t 8 -M ~/genomes/hg19/bwa-indexes/hg19-female.fa A-N4293-2.end1_val_1.fq.gz A-N4293-2.end2_val_2.fq.gz | ~/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT ~/genomes/hg19/sequence/hg19.fa - | ~/programs/samtools-0.1.18/samtools sort - A-N4293-2.2x75mers-trimmed.bwa-mem.hg19-female
bwa mem -t 8 -M ~/genomes/hg19/bwa-indexes/hg19-female.fa A-N4371-1.end1_val_1.fq.gz A-N4371-1.end2_val_2.fq.gz | ~/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT ~/genomes/hg19/sequence/hg19.fa - | ~/programs/samtools-0.1.18/samtools sort - A-N4371-1.2x75mers-trimmed.bwa-mem.hg19-female
bwa mem -t 8 -M ~/genomes/hg19/bwa-indexes/hg19-female.fa A-N4371-2.end1_val_1.fq.gz A-N4371-2.end2_val_2.fq.gz | ~/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT ~/genomes/hg19/sequence/hg19.fa - | ~/programs/samtools-0.1.18/samtools sort - A-N4371-2.2x75mers-trimmed.bwa-mem.hg19-female
bwa mem -t 8 -M ~/genomes/hg19/bwa-indexes/hg19-female.fa KO-13004-1.end1_val_1.fq.gz KO-13004-1.end2_val_2.fq.gz | ~/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT ~/genomes/hg19/sequence/hg19.fa - | ~/programs/samtools-0.1.18/samtools sort - KO-13004-1.2x75mers-trimmed.bwa-mem.hg19-female
bwa mem -t 8 -M ~/genomes/hg19/bwa-indexes/hg19-female.fa KO-13004-2.end1_val_1.fq.gz KO-13004-2.end2_val_2.fq.gz | ~/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT ~/genomes/hg19/sequence/hg19.fa - | ~/programs/samtools-0.1.18/samtools sort - KO-13004-2.2x75mers-trimmed.bwa-mem.hg19-female
bwa mem -t 8 -M ~/genomes/hg19/bwa-indexes/hg19-female.fa KO-13006-1.end1_val_1.fq.gz KO-13006-1.end2_val_2.fq.gz | ~/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT ~/genomes/hg19/sequence/hg19.fa - | ~/programs/samtools-0.1.18/samtools sort - KO-13006-1.2x75mers-trimmed.bwa-mem.hg19-female
bwa mem -t 8 -M ~/genomes/hg19/bwa-indexes/hg19-female.fa KO-13006-2.end1_val_1.fq.gz KO-13006-2.end2_val_2.fq.gz | ~/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT ~/genomes/hg19/sequence/hg19.fa - | ~/programs/samtools-0.1.18/samtools sort - KO-13006-2.2x75mers-trimmed.bwa-mem.hg19-female
bwa mem -t 8 -M ~/genomes/hg19/bwa-indexes/hg19-female.fa KO-N4293-1.end1_val_1.fq.gz KO-N4293-1.end2_val_2.fq.gz | ~/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT ~/genomes/hg19/sequence/hg19.fa - | ~/programs/samtools-0.1.18/samtools sort - KO-N4293-1.2x75mers-trimmed.bwa-mem.hg19-female
bwa mem -t 8 -M ~/genomes/hg19/bwa-indexes/hg19-female.fa KO-N4293-2.end1_val_1.fq.gz KO-N4293-2.end2_val_2.fq.gz | ~/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT ~/genomes/hg19/sequence/hg19.fa - | ~/programs/samtools-0.1.18/samtools sort - KO-N4293-2.2x75mers-trimmed.bwa-mem.hg19-female
bwa mem -t 8 -M ~/genomes/hg19/bwa-indexes/hg19-female.fa KO-N4371-1.end1_val_1.fq.gz KO-N4371-1.end2_val_2.fq.gz | ~/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT ~/genomes/hg19/sequence/hg19.fa - | ~/programs/samtools-0.1.18/samtools sort - KO-N4371-1.2x75mers-trimmed.bwa-mem.hg19-female
bwa mem -t 8 -M ~/genomes/hg19/bwa-indexes/hg19-female.fa KO-N4371-2.end1_val_1.fq.gz KO-N4371-2.end2_val_2.fq.gz | ~/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT ~/genomes/hg19/sequence/hg19.fa - | ~/programs/samtools-0.1.18/samtools sort - KO-N4371-2.2x75mers-trimmed.bwa-mem.hg19-female