/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.17/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa DB115_Br2-CRR994956.read1.paired.fastq.gz DB115_Br2-CRR994956.read2.paired.fastq.gz | egrep -v MT | ~/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa - |  ~/programs/samtools-0.1.18/samtools sort - DB115_Br2-CRR994956.2x36mers.noMT.bwa.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.17/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa DB115_Br3-CRR994957.read1.paired.fastq.gz DB115_Br3-CRR994957.read2.paired.fastq.gz | egrep -v MT | ~/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa - |  ~/programs/samtools-0.1.18/samtools sort - DB115_Br3-CRR994957.2x36mers.noMT.bwa.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.17/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa DB115_Li2-CRR994959.read1.paired.fastq.gz DB115_Li2-CRR994959.read2.paired.fastq.gz | egrep -v MT | ~/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa - |  ~/programs/samtools-0.1.18/samtools sort - DB115_Li2-CRR994959.2x36mers.noMT.bwa.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.17/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa DB115_Li3-CRR994960.read1.paired.fastq.gz DB115_Li3-CRR994960.read2.paired.fastq.gz | egrep -v MT | ~/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa - |  ~/programs/samtools-0.1.18/samtools sort - DB115_Li3-CRR994960.2x36mers.noMT.bwa.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.17/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa DB115_Mu1-CRR994961.read1.paired.fastq.gz DB115_Mu1-CRR994961.read2.paired.fastq.gz | egrep -v MT | ~/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa - |  ~/programs/samtools-0.1.18/samtools sort - DB115_Mu1-CRR994961.2x36mers.noMT.bwa.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.17/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa DB115_Mu2-CRR994962.read1.paired.fastq.gz DB115_Mu2-CRR994962.read2.paired.fastq.gz | egrep -v MT | ~/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa - |  ~/programs/samtools-0.1.18/samtools sort - DB115_Mu2-CRR994962.2x36mers.noMT.bwa.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.17/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa DB115_Mu3-CRR994963.read1.paired.fastq.gz DB115_Mu3-CRR994963.read2.paired.fastq.gz | egrep -v MT | ~/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa - |  ~/programs/samtools-0.1.18/samtools sort - DB115_Mu3-CRR994963.2x36mers.noMT.bwa.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.17/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa DB168_E_Br1-CRR994964.read1.paired.fastq.gz DB168_E_Br1-CRR994964.read2.paired.fastq.gz | egrep -v MT | ~/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa - |  ~/programs/samtools-0.1.18/samtools sort - DB168_E_Br1-CRR994964.2x36mers.noMT.bwa.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.17/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa DB168_E_Li1-CRR994965.read1.paired.fastq.gz DB168_E_Li1-CRR994965.read2.paired.fastq.gz | egrep -v MT | ~/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa - |  ~/programs/samtools-0.1.18/samtools sort - DB168_E_Li1-CRR994965.2x36mers.noMT.bwa.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.17/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa DB168_I_Br2-CRR994967.read1.paired.fastq.gz DB168_I_Br2-CRR994967.read2.paired.fastq.gz | egrep -v MT | ~/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa - |  ~/programs/samtools-0.1.18/samtools sort - DB168_I_Br2-CRR994967.2x36mers.noMT.bwa.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.17/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa DB168_I_Li2-CRR994968.read1.paired.fastq.gz DB168_I_Li2-CRR994968.read2.paired.fastq.gz | egrep -v MT | ~/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa - |  ~/programs/samtools-0.1.18/samtools sort - DB168_I_Li2-CRR994968.2x36mers.noMT.bwa.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.17/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa DB168_I_Mu2-CRR994969.read1.paired.fastq.gz DB168_I_Mu2-CRR994969.read2.paired.fastq.gz | egrep -v MT | ~/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa - |  ~/programs/samtools-0.1.18/samtools sort - DB168_I_Mu2-CRR994969.2x36mers.noMT.bwa.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.17/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa DB168_J_Br3-CRR994970.read1.paired.fastq.gz DB168_J_Br3-CRR994970.read2.paired.fastq.gz | egrep -v MT | ~/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa - |  ~/programs/samtools-0.1.18/samtools sort - DB168_J_Br3-CRR994970.2x36mers.noMT.bwa.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.17/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa DB168_J_Li3-CRR994971.read1.paired.fastq.gz DB168_J_Li3-CRR994971.read2.paired.fastq.gz | egrep -v MT | ~/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa - |  ~/programs/samtools-0.1.18/samtools sort - DB168_J_Li3-CRR994971.2x36mers.noMT.bwa.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.17/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa DB168_J_Mu3-CRR994972.read1.paired.fastq.gz DB168_J_Mu3-CRR994972.read2.paired.fastq.gz | egrep -v MT | ~/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa - |  ~/programs/samtools-0.1.18/samtools sort - DB168_J_Mu3-CRR994972.2x36mers.noMT.bwa.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.17/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa DB40_Br1-CRR994973.read1.paired.fastq.gz DB40_Br1-CRR994973.read2.paired.fastq.gz | egrep -v MT | ~/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa - |  ~/programs/samtools-0.1.18/samtools sort - DB40_Br1-CRR994973.2x36mers.noMT.bwa.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.17/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa DB40_Li1-CRR994976.read1.paired.fastq.gz DB40_Li1-CRR994976.read2.paired.fastq.gz | egrep -v MT | ~/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa - |  ~/programs/samtools-0.1.18/samtools sort - DB40_Li1-CRR994976.2x36mers.noMT.bwa.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.17/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa DB40_Li2-CRR994977.read1.paired.fastq.gz DB40_Li2-CRR994977.read2.paired.fastq.gz | egrep -v MT | ~/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa - |  ~/programs/samtools-0.1.18/samtools sort - DB40_Li2-CRR994977.2x36mers.noMT.bwa.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.17/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa DB40_Li3-CRR994978.read1.paired.fastq.gz DB40_Li3-CRR994978.read2.paired.fastq.gz | egrep -v MT | ~/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa - |  ~/programs/samtools-0.1.18/samtools sort - DB40_Li3-CRR994978.2x36mers.noMT.bwa.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.17/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa DB40_Mu1-CRR994979.read1.paired.fastq.gz DB40_Mu1-CRR994979.read2.paired.fastq.gz | egrep -v MT | ~/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa - |  ~/programs/samtools-0.1.18/samtools sort - DB40_Mu1-CRR994979.2x36mers.noMT.bwa.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.17/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa DB40_Mu2-CRR994980.read1.paired.fastq.gz DB40_Mu2-CRR994980.read2.paired.fastq.gz | egrep -v MT | ~/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa - |  ~/programs/samtools-0.1.18/samtools sort - DB40_Mu2-CRR994980.2x36mers.noMT.bwa.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.17/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa DB40_Mu3-CRR994981.read1.paired.fastq.gz DB40_Mu3-CRR994981.read2.paired.fastq.gz | egrep -v MT | ~/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa - |  ~/programs/samtools-0.1.18/samtools sort - DB40_Mu3-CRR994981.2x36mers.noMT.bwa.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.17/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa DB40_Pl1-CRR994982.read1.paired.fastq.gz DB40_Pl1-CRR994982.read2.paired.fastq.gz | egrep -v MT | ~/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa - |  ~/programs/samtools-0.1.18/samtools sort - DB40_Pl1-CRR994982.2x36mers.noMT.bwa.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.17/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa DB40_Pl2-CRR994983.read1.paired.fastq.gz DB40_Pl2-CRR994983.read2.paired.fastq.gz | egrep -v MT | ~/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa - |  ~/programs/samtools-0.1.18/samtools sort - DB40_Pl2-CRR994983.2x36mers.noMT.bwa.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.17/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa DB40_Pl3-CRR994984.read1.paired.fastq.gz DB40_Pl3-CRR994984.read2.paired.fastq.gz | egrep -v MT | ~/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa - |  ~/programs/samtools-0.1.18/samtools sort - DB40_Pl3-CRR994984.2x36mers.noMT.bwa.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.17/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa DB70_Br1-CRR994985.read1.paired.fastq.gz DB70_Br1-CRR994985.read2.paired.fastq.gz | egrep -v MT | ~/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa - |  ~/programs/samtools-0.1.18/samtools sort - DB70_Br1-CRR994985.2x36mers.noMT.bwa.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.17/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa DB70_Br3-CRR994987.read1.paired.fastq.gz DB70_Br3-CRR994987.read2.paired.fastq.gz | egrep -v MT | ~/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa - |  ~/programs/samtools-0.1.18/samtools sort - DB70_Br3-CRR994987.2x36mers.noMT.bwa.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.17/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa DB70_Li2-CRR994989.read1.paired.fastq.gz DB70_Li2-CRR994989.read2.paired.fastq.gz | egrep -v MT | ~/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa - |  ~/programs/samtools-0.1.18/samtools sort - DB70_Li2-CRR994989.2x36mers.noMT.bwa.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.17/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa DB70_Li3-CRR994990.read1.paired.fastq.gz DB70_Li3-CRR994990.read2.paired.fastq.gz | egrep -v MT | ~/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa - |  ~/programs/samtools-0.1.18/samtools sort - DB70_Li3-CRR994990.2x36mers.noMT.bwa.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.17/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa DB70_Mu1-CRR994991.read1.paired.fastq.gz DB70_Mu1-CRR994991.read2.paired.fastq.gz | egrep -v MT | ~/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa - |  ~/programs/samtools-0.1.18/samtools sort - DB70_Mu1-CRR994991.2x36mers.noMT.bwa.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.17/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa DB70_Mu2-CRR994992.read1.paired.fastq.gz DB70_Mu2-CRR994992.read2.paired.fastq.gz | egrep -v MT | ~/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa - |  ~/programs/samtools-0.1.18/samtools sort - DB70_Mu2-CRR994992.2x36mers.noMT.bwa.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.17/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa DB70_Mu3-CRR994993.read1.paired.fastq.gz DB70_Mu3-CRR994993.read2.paired.fastq.gz | egrep -v MT | ~/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa - |  ~/programs/samtools-0.1.18/samtools sort - DB70_Mu3-CRR994993.2x36mers.noMT.bwa.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.17/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa DB70_Pl1-CRR994994.read1.paired.fastq.gz DB70_Pl1-CRR994994.read2.paired.fastq.gz | egrep -v MT | ~/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa - |  ~/programs/samtools-0.1.18/samtools sort - DB70_Pl1-CRR994994.2x36mers.noMT.bwa.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.17/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa DS115_Br1-CRR994995.read1.paired.fastq.gz DS115_Br1-CRR994995.read2.paired.fastq.gz | egrep -v MT | ~/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa - |  ~/programs/samtools-0.1.18/samtools sort - DS115_Br1-CRR994995.2x36mers.noMT.bwa.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.17/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa DS115_Br2-CRR994996.read1.paired.fastq.gz DS115_Br2-CRR994996.read2.paired.fastq.gz | egrep -v MT | ~/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa - |  ~/programs/samtools-0.1.18/samtools sort - DS115_Br2-CRR994996.2x36mers.noMT.bwa.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.17/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa DS115_Br3-CRR994997.read1.paired.fastq.gz DS115_Br3-CRR994997.read2.paired.fastq.gz | egrep -v MT | ~/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa - |  ~/programs/samtools-0.1.18/samtools sort - DS115_Br3-CRR994997.2x36mers.noMT.bwa.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.17/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa DS115_Li1-CRR994998.read1.paired.fastq.gz DS115_Li1-CRR994998.read2.paired.fastq.gz | egrep -v MT | ~/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa - |  ~/programs/samtools-0.1.18/samtools sort - DS115_Li1-CRR994998.2x36mers.noMT.bwa.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.17/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa DS115_Li2-CRR994999.read1.paired.fastq.gz DS115_Li2-CRR994999.read2.paired.fastq.gz | egrep -v MT | ~/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa - |  ~/programs/samtools-0.1.18/samtools sort - DS115_Li2-CRR994999.2x36mers.noMT.bwa.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.17/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa DS115_Li3-CRR995000.read1.paired.fastq.gz DS115_Li3-CRR995000.read2.paired.fastq.gz | egrep -v MT | ~/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa - |  ~/programs/samtools-0.1.18/samtools sort - DS115_Li3-CRR995000.2x36mers.noMT.bwa.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.17/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa DS115_Mu1-CRR995001.read1.paired.fastq.gz DS115_Mu1-CRR995001.read2.paired.fastq.gz | egrep -v MT | ~/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa - |  ~/programs/samtools-0.1.18/samtools sort - DS115_Mu1-CRR995001.2x36mers.noMT.bwa.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.17/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa DS115_Mu2-CRR995002.read1.paired.fastq.gz DS115_Mu2-CRR995002.read2.paired.fastq.gz | egrep -v MT | ~/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa - |  ~/programs/samtools-0.1.18/samtools sort - DS115_Mu2-CRR995002.2x36mers.noMT.bwa.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.17/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa DS115_Mu3-CRR995003.read1.paired.fastq.gz DS115_Mu3-CRR995003.read2.paired.fastq.gz | egrep -v MT | ~/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa - |  ~/programs/samtools-0.1.18/samtools sort - DS115_Mu3-CRR995003.2x36mers.noMT.bwa.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.17/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa DS168_M_Br1-CRR995004.read1.paired.fastq.gz DS168_M_Br1-CRR995004.read2.paired.fastq.gz | egrep -v MT | ~/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa - |  ~/programs/samtools-0.1.18/samtools sort - DS168_M_Br1-CRR995004.2x36mers.noMT.bwa.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.17/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa DS168_M_Li1-CRR995005.read1.paired.fastq.gz DS168_M_Li1-CRR995005.read2.paired.fastq.gz | egrep -v MT | ~/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa - |  ~/programs/samtools-0.1.18/samtools sort - DS168_M_Li1-CRR995005.2x36mers.noMT.bwa.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.17/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa DS168_N_Br2-CRR995007.read1.paired.fastq.gz DS168_N_Br2-CRR995007.read2.paired.fastq.gz | egrep -v MT | ~/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa - |  ~/programs/samtools-0.1.18/samtools sort - DS168_N_Br2-CRR995007.2x36mers.noMT.bwa.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.17/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa DS168_N_Li2-CRR995008.read1.paired.fastq.gz DS168_N_Li2-CRR995008.read2.paired.fastq.gz | egrep -v MT | ~/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa - |  ~/programs/samtools-0.1.18/samtools sort - DS168_N_Li2-CRR995008.2x36mers.noMT.bwa.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.17/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa DS168_N_Mu2-CRR995009.read1.paired.fastq.gz DS168_N_Mu2-CRR995009.read2.paired.fastq.gz | egrep -v MT | ~/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa - |  ~/programs/samtools-0.1.18/samtools sort - DS168_N_Mu2-CRR995009.2x36mers.noMT.bwa.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.17/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa DS168_O_Br3-CRR995010.read1.paired.fastq.gz DS168_O_Br3-CRR995010.read2.paired.fastq.gz | egrep -v MT | ~/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa - |  ~/programs/samtools-0.1.18/samtools sort - DS168_O_Br3-CRR995010.2x36mers.noMT.bwa.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.17/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa DS168_O_Li3-CRR995011.read1.paired.fastq.gz DS168_O_Li3-CRR995011.read2.paired.fastq.gz | egrep -v MT | ~/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa - |  ~/programs/samtools-0.1.18/samtools sort - DS168_O_Li3-CRR995011.2x36mers.noMT.bwa.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.17/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa DS40_Br1-CRR995013.read1.paired.fastq.gz DS40_Br1-CRR995013.read2.paired.fastq.gz | egrep -v MT | ~/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa - |  ~/programs/samtools-0.1.18/samtools sort - DS40_Br1-CRR995013.2x36mers.noMT.bwa.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.17/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa DS40_Br2-CRR995014.read1.paired.fastq.gz DS40_Br2-CRR995014.read2.paired.fastq.gz | egrep -v MT | ~/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa - |  ~/programs/samtools-0.1.18/samtools sort - DS40_Br2-CRR995014.2x36mers.noMT.bwa.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.17/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa DS40_Br3-CRR995015.read1.paired.fastq.gz DS40_Br3-CRR995015.read2.paired.fastq.gz | egrep -v MT | ~/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa - |  ~/programs/samtools-0.1.18/samtools sort - DS40_Br3-CRR995015.2x36mers.noMT.bwa.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.17/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa DS40_Li2-CRR995016.read1.paired.fastq.gz DS40_Li2-CRR995016.read2.paired.fastq.gz | egrep -v MT | ~/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa - |  ~/programs/samtools-0.1.18/samtools sort - DS40_Li2-CRR995016.2x36mers.noMT.bwa.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.17/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa DS40_Li3-CRR995017.read1.paired.fastq.gz DS40_Li3-CRR995017.read2.paired.fastq.gz | egrep -v MT | ~/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa - |  ~/programs/samtools-0.1.18/samtools sort - DS40_Li3-CRR995017.2x36mers.noMT.bwa.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.17/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa DS40_Mu1-CRR995018.read1.paired.fastq.gz DS40_Mu1-CRR995018.read2.paired.fastq.gz | egrep -v MT | ~/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa - |  ~/programs/samtools-0.1.18/samtools sort - DS40_Mu1-CRR995018.2x36mers.noMT.bwa.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.17/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa DS40_Mu2-CRR995019.read1.paired.fastq.gz DS40_Mu2-CRR995019.read2.paired.fastq.gz | egrep -v MT | ~/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa - |  ~/programs/samtools-0.1.18/samtools sort - DS40_Mu2-CRR995019.2x36mers.noMT.bwa.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.17/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa DS40_Mu3-CRR995020.read1.paired.fastq.gz DS40_Mu3-CRR995020.read2.paired.fastq.gz | egrep -v MT | ~/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa - |  ~/programs/samtools-0.1.18/samtools sort - DS40_Mu3-CRR995020.2x36mers.noMT.bwa.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.17/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa DS40_Pl1-CRR995021.read1.paired.fastq.gz DS40_Pl1-CRR995021.read2.paired.fastq.gz | egrep -v MT | ~/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa - |  ~/programs/samtools-0.1.18/samtools sort - DS40_Pl1-CRR995021.2x36mers.noMT.bwa.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.17/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa DS40_Pl2-CRR995022.read1.paired.fastq.gz DS40_Pl2-CRR995022.read2.paired.fastq.gz | egrep -v MT | ~/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa - |  ~/programs/samtools-0.1.18/samtools sort - DS40_Pl2-CRR995022.2x36mers.noMT.bwa.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.17/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa DS40_Pl3-CRR995023.read1.paired.fastq.gz DS40_Pl3-CRR995023.read2.paired.fastq.gz | egrep -v MT | ~/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa - |  ~/programs/samtools-0.1.18/samtools sort - DS40_Pl3-CRR995023.2x36mers.noMT.bwa.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.17/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa DS70_Br1-CRR995024.read1.paired.fastq.gz DS70_Br1-CRR995024.read2.paired.fastq.gz | egrep -v MT | ~/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa - |  ~/programs/samtools-0.1.18/samtools sort - DS70_Br1-CRR995024.2x36mers.noMT.bwa.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.17/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa DS70_Br2-CRR995025.read1.paired.fastq.gz DS70_Br2-CRR995025.read2.paired.fastq.gz | egrep -v MT | ~/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa - |  ~/programs/samtools-0.1.18/samtools sort - DS70_Br2-CRR995025.2x36mers.noMT.bwa.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.17/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa DS70_Br3-CRR995026.read1.paired.fastq.gz DS70_Br3-CRR995026.read2.paired.fastq.gz | egrep -v MT | ~/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa - |  ~/programs/samtools-0.1.18/samtools sort - DS70_Br3-CRR995026.2x36mers.noMT.bwa.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.17/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa DS70_Li1-CRR995027.read1.paired.fastq.gz DS70_Li1-CRR995027.read2.paired.fastq.gz | egrep -v MT | ~/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa - |  ~/programs/samtools-0.1.18/samtools sort - DS70_Li1-CRR995027.2x36mers.noMT.bwa.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.17/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa DS70_Li2-CRR995028.read1.paired.fastq.gz DS70_Li2-CRR995028.read2.paired.fastq.gz | egrep -v MT | ~/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa - |  ~/programs/samtools-0.1.18/samtools sort - DS70_Li2-CRR995028.2x36mers.noMT.bwa.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.17/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa DS70_Li3-CRR995029.read1.paired.fastq.gz DS70_Li3-CRR995029.read2.paired.fastq.gz | egrep -v MT | ~/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa - |  ~/programs/samtools-0.1.18/samtools sort - DS70_Li3-CRR995029.2x36mers.noMT.bwa.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.17/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa DS70_Mu1-CRR995030.read1.paired.fastq.gz DS70_Mu1-CRR995030.read2.paired.fastq.gz | egrep -v MT | ~/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa - |  ~/programs/samtools-0.1.18/samtools sort - DS70_Mu1-CRR995030.2x36mers.noMT.bwa.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.17/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa DS70_Mu2-CRR995031.read1.paired.fastq.gz DS70_Mu2-CRR995031.read2.paired.fastq.gz | egrep -v MT | ~/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa - |  ~/programs/samtools-0.1.18/samtools sort - DS70_Mu2-CRR995031.2x36mers.noMT.bwa.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.17/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa DS70_Mu3-CRR995032.read1.paired.fastq.gz DS70_Mu3-CRR995032.read2.paired.fastq.gz | egrep -v MT | ~/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa - |  ~/programs/samtools-0.1.18/samtools sort - DS70_Mu3-CRR995032.2x36mers.noMT.bwa.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.17/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa DS70_Pl1-CRR995033.read1.paired.fastq.gz DS70_Pl1-CRR995033.read2.paired.fastq.gz | egrep -v MT | ~/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa - |  ~/programs/samtools-0.1.18/samtools sort - DS70_Pl1-CRR995033.2x36mers.noMT.bwa.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.17/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa DS70_Pl3-CRR995034.read1.paired.fastq.gz DS70_Pl3-CRR995034.read2.paired.fastq.gz | egrep -v MT | ~/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa - |  ~/programs/samtools-0.1.18/samtools sort - DS70_Pl3-CRR995034.2x36mers.noMT.bwa.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.17/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa LB115_Br1-CRR995035.read1.paired.fastq.gz LB115_Br1-CRR995035.read2.paired.fastq.gz | egrep -v MT | ~/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa - |  ~/programs/samtools-0.1.18/samtools sort - LB115_Br1-CRR995035.2x36mers.noMT.bwa.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.17/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa LB115_Br2-CRR995036.read1.paired.fastq.gz LB115_Br2-CRR995036.read2.paired.fastq.gz | egrep -v MT | ~/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa - |  ~/programs/samtools-0.1.18/samtools sort - LB115_Br2-CRR995036.2x36mers.noMT.bwa.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.17/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa LB115_Br3-CRR995037.read1.paired.fastq.gz LB115_Br3-CRR995037.read2.paired.fastq.gz | egrep -v MT | ~/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa - |  ~/programs/samtools-0.1.18/samtools sort - LB115_Br3-CRR995037.2x36mers.noMT.bwa.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.17/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa LB115_Li1-CRR995038.read1.paired.fastq.gz LB115_Li1-CRR995038.read2.paired.fastq.gz | egrep -v MT | ~/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa - |  ~/programs/samtools-0.1.18/samtools sort - LB115_Li1-CRR995038.2x36mers.noMT.bwa.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.17/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa LB115_Li2-CRR995039.read1.paired.fastq.gz LB115_Li2-CRR995039.read2.paired.fastq.gz | egrep -v MT | ~/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa - |  ~/programs/samtools-0.1.18/samtools sort - LB115_Li2-CRR995039.2x36mers.noMT.bwa.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.17/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa LB115_Li3-CRR995040.read1.paired.fastq.gz LB115_Li3-CRR995040.read2.paired.fastq.gz | egrep -v MT | ~/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa - |  ~/programs/samtools-0.1.18/samtools sort - LB115_Li3-CRR995040.2x36mers.noMT.bwa.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.17/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa LB115_Mu1-CRR995041.read1.paired.fastq.gz LB115_Mu1-CRR995041.read2.paired.fastq.gz | egrep -v MT | ~/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa - |  ~/programs/samtools-0.1.18/samtools sort - LB115_Mu1-CRR995041.2x36mers.noMT.bwa.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.17/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa LB115_Mu2-CRR995042.read1.paired.fastq.gz LB115_Mu2-CRR995042.read2.paired.fastq.gz | egrep -v MT | ~/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa - |  ~/programs/samtools-0.1.18/samtools sort - LB115_Mu2-CRR995042.2x36mers.noMT.bwa.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.17/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa LB115_Mu3-CRR995043.read1.paired.fastq.gz LB115_Mu3-CRR995043.read2.paired.fastq.gz | egrep -v MT | ~/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa - |  ~/programs/samtools-0.1.18/samtools sort - LB115_Mu3-CRR995043.2x36mers.noMT.bwa.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.17/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa LB168_F_Br2-CRR995044.read1.paired.fastq.gz LB168_F_Br2-CRR995044.read2.paired.fastq.gz | egrep -v MT | ~/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa - |  ~/programs/samtools-0.1.18/samtools sort - LB168_F_Br2-CRR995044.2x36mers.noMT.bwa.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.17/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa LB168_F_Li2-CRR995045.read1.paired.fastq.gz LB168_F_Li2-CRR995045.read2.paired.fastq.gz | egrep -v MT | ~/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa - |  ~/programs/samtools-0.1.18/samtools sort - LB168_F_Li2-CRR995045.2x36mers.noMT.bwa.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.17/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa LB168_F_Mu2-CRR995046.read1.paired.fastq.gz LB168_F_Mu2-CRR995046.read2.paired.fastq.gz | egrep -v MT | ~/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa - |  ~/programs/samtools-0.1.18/samtools sort - LB168_F_Mu2-CRR995046.2x36mers.noMT.bwa.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.17/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa LB168_G_Br1-CRR995047.read1.paired.fastq.gz LB168_G_Br1-CRR995047.read2.paired.fastq.gz | egrep -v MT | ~/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa - |  ~/programs/samtools-0.1.18/samtools sort - LB168_G_Br1-CRR995047.2x36mers.noMT.bwa.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.17/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa LB168_G_Li1-CRR995048.read1.paired.fastq.gz LB168_G_Li1-CRR995048.read2.paired.fastq.gz | egrep -v MT | ~/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa - |  ~/programs/samtools-0.1.18/samtools sort - LB168_G_Li1-CRR995048.2x36mers.noMT.bwa.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.17/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa LB168_G_Mu1-CRR995049.read1.paired.fastq.gz LB168_G_Mu1-CRR995049.read2.paired.fastq.gz | egrep -v MT | ~/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa - |  ~/programs/samtools-0.1.18/samtools sort - LB168_G_Mu1-CRR995049.2x36mers.noMT.bwa.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.17/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa LB168_H_Br3-CRR995050.read1.paired.fastq.gz LB168_H_Br3-CRR995050.read2.paired.fastq.gz | egrep -v MT | ~/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa - |  ~/programs/samtools-0.1.18/samtools sort - LB168_H_Br3-CRR995050.2x36mers.noMT.bwa.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.17/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa LB168_H_Li3-CRR995051.read1.paired.fastq.gz LB168_H_Li3-CRR995051.read2.paired.fastq.gz | egrep -v MT | ~/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa - |  ~/programs/samtools-0.1.18/samtools sort - LB168_H_Li3-CRR995051.2x36mers.noMT.bwa.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.17/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa LB168_H_Mu3-CRR995052.read1.paired.fastq.gz LB168_H_Mu3-CRR995052.read2.paired.fastq.gz | egrep -v MT | ~/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa - |  ~/programs/samtools-0.1.18/samtools sort - LB168_H_Mu3-CRR995052.2x36mers.noMT.bwa.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.17/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa LB40_Br1-CRR995053.read1.paired.fastq.gz LB40_Br1-CRR995053.read2.paired.fastq.gz | egrep -v MT | ~/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa - |  ~/programs/samtools-0.1.18/samtools sort - LB40_Br1-CRR995053.2x36mers.noMT.bwa.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.17/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa LB40_Br3-CRR995055.read1.paired.fastq.gz LB40_Br3-CRR995055.read2.paired.fastq.gz | egrep -v MT | ~/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa - |  ~/programs/samtools-0.1.18/samtools sort - LB40_Br3-CRR995055.2x36mers.noMT.bwa.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.17/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa LB40_Li1-CRR995056.read1.paired.fastq.gz LB40_Li1-CRR995056.read2.paired.fastq.gz | egrep -v MT | ~/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa - |  ~/programs/samtools-0.1.18/samtools sort - LB40_Li1-CRR995056.2x36mers.noMT.bwa.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.17/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa LB40_Li2-CRR995057.read1.paired.fastq.gz LB40_Li2-CRR995057.read2.paired.fastq.gz | egrep -v MT | ~/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa - |  ~/programs/samtools-0.1.18/samtools sort - LB40_Li2-CRR995057.2x36mers.noMT.bwa.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.17/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa LB40_Li3-CRR995058.read1.paired.fastq.gz LB40_Li3-CRR995058.read2.paired.fastq.gz | egrep -v MT | ~/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa - |  ~/programs/samtools-0.1.18/samtools sort - LB40_Li3-CRR995058.2x36mers.noMT.bwa.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.17/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa LB40_Mu2-CRR995060.read1.paired.fastq.gz LB40_Mu2-CRR995060.read2.paired.fastq.gz | egrep -v MT | ~/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa - |  ~/programs/samtools-0.1.18/samtools sort - LB40_Mu2-CRR995060.2x36mers.noMT.bwa.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.17/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa LB40_Mu3-CRR995061.read1.paired.fastq.gz LB40_Mu3-CRR995061.read2.paired.fastq.gz | egrep -v MT | ~/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa - |  ~/programs/samtools-0.1.18/samtools sort - LB40_Mu3-CRR995061.2x36mers.noMT.bwa.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.17/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa LB40_Pl1-CRR995062.read1.paired.fastq.gz LB40_Pl1-CRR995062.read2.paired.fastq.gz | egrep -v MT | ~/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa - |  ~/programs/samtools-0.1.18/samtools sort - LB40_Pl1-CRR995062.2x36mers.noMT.bwa.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.17/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa LB40_Pl2-CRR995063.read1.paired.fastq.gz LB40_Pl2-CRR995063.read2.paired.fastq.gz | egrep -v MT | ~/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa - |  ~/programs/samtools-0.1.18/samtools sort - LB40_Pl2-CRR995063.2x36mers.noMT.bwa.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.17/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa LB40_Pl3-CRR995064.read1.paired.fastq.gz LB40_Pl3-CRR995064.read2.paired.fastq.gz | egrep -v MT | ~/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa - |  ~/programs/samtools-0.1.18/samtools sort - LB40_Pl3-CRR995064.2x36mers.noMT.bwa.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.17/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa LB70_Br1-CRR995065.read1.paired.fastq.gz LB70_Br1-CRR995065.read2.paired.fastq.gz | egrep -v MT | ~/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa - |  ~/programs/samtools-0.1.18/samtools sort - LB70_Br1-CRR995065.2x36mers.noMT.bwa.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.17/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa LB70_Br2-CRR995066.read1.paired.fastq.gz LB70_Br2-CRR995066.read2.paired.fastq.gz | egrep -v MT | ~/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa - |  ~/programs/samtools-0.1.18/samtools sort - LB70_Br2-CRR995066.2x36mers.noMT.bwa.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.17/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa LB70_Br3-CRR995067.read1.paired.fastq.gz LB70_Br3-CRR995067.read2.paired.fastq.gz | egrep -v MT | ~/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa - |  ~/programs/samtools-0.1.18/samtools sort - LB70_Br3-CRR995067.2x36mers.noMT.bwa.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.17/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa LB70_Li1-CRR995068.read1.paired.fastq.gz LB70_Li1-CRR995068.read2.paired.fastq.gz | egrep -v MT | ~/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa - |  ~/programs/samtools-0.1.18/samtools sort - LB70_Li1-CRR995068.2x36mers.noMT.bwa.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.17/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa LB70_Li2-CRR995069.read1.paired.fastq.gz LB70_Li2-CRR995069.read2.paired.fastq.gz | egrep -v MT | ~/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa - |  ~/programs/samtools-0.1.18/samtools sort - LB70_Li2-CRR995069.2x36mers.noMT.bwa.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.17/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa LB70_Li3-CRR995070.read1.paired.fastq.gz LB70_Li3-CRR995070.read2.paired.fastq.gz | egrep -v MT | ~/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa - |  ~/programs/samtools-0.1.18/samtools sort - LB70_Li3-CRR995070.2x36mers.noMT.bwa.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.17/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa LB70_Mu1-CRR995071.read1.paired.fastq.gz LB70_Mu1-CRR995071.read2.paired.fastq.gz | egrep -v MT | ~/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa - |  ~/programs/samtools-0.1.18/samtools sort - LB70_Mu1-CRR995071.2x36mers.noMT.bwa.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.17/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa LB70_Mu2-CRR995072.read1.paired.fastq.gz LB70_Mu2-CRR995072.read2.paired.fastq.gz | egrep -v MT | ~/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa - |  ~/programs/samtools-0.1.18/samtools sort - LB70_Mu2-CRR995072.2x36mers.noMT.bwa.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.17/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa LB70_Mu3-CRR995073.read1.paired.fastq.gz LB70_Mu3-CRR995073.read2.paired.fastq.gz | egrep -v MT | ~/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa - |  ~/programs/samtools-0.1.18/samtools sort - LB70_Mu3-CRR995073.2x36mers.noMT.bwa.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.17/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa LB70_Pl1-CRR995074.read1.paired.fastq.gz LB70_Pl1-CRR995074.read2.paired.fastq.gz | egrep -v MT | ~/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa - |  ~/programs/samtools-0.1.18/samtools sort - LB70_Pl1-CRR995074.2x36mers.noMT.bwa.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.17/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa LB70_Pl2-CRR995075.read1.paired.fastq.gz LB70_Pl2-CRR995075.read2.paired.fastq.gz | egrep -v MT | ~/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa - |  ~/programs/samtools-0.1.18/samtools sort - LB70_Pl2-CRR995075.2x36mers.noMT.bwa.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.17/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa LB70_Pl3-CRR995076.read1.paired.fastq.gz LB70_Pl3-CRR995076.read2.paired.fastq.gz | egrep -v MT | ~/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa - |  ~/programs/samtools-0.1.18/samtools sort - LB70_Pl3-CRR995076.2x36mers.noMT.bwa.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.17/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa LS115_Br1-CRR995077.read1.paired.fastq.gz LS115_Br1-CRR995077.read2.paired.fastq.gz | egrep -v MT | ~/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa - |  ~/programs/samtools-0.1.18/samtools sort - LS115_Br1-CRR995077.2x36mers.noMT.bwa.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.17/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa LS115_Br2-CRR995078.read1.paired.fastq.gz LS115_Br2-CRR995078.read2.paired.fastq.gz | egrep -v MT | ~/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa - |  ~/programs/samtools-0.1.18/samtools sort - LS115_Br2-CRR995078.2x36mers.noMT.bwa.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.17/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa LS115_Br3-CRR995079.read1.paired.fastq.gz LS115_Br3-CRR995079.read2.paired.fastq.gz | egrep -v MT | ~/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa - |  ~/programs/samtools-0.1.18/samtools sort - LS115_Br3-CRR995079.2x36mers.noMT.bwa.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.17/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa LS115_Li1-CRR995080.read1.paired.fastq.gz LS115_Li1-CRR995080.read2.paired.fastq.gz | egrep -v MT | ~/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa - |  ~/programs/samtools-0.1.18/samtools sort - LS115_Li1-CRR995080.2x36mers.noMT.bwa.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.17/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa LS115_Li2-CRR995081.read1.paired.fastq.gz LS115_Li2-CRR995081.read2.paired.fastq.gz | egrep -v MT | ~/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa - |  ~/programs/samtools-0.1.18/samtools sort - LS115_Li2-CRR995081.2x36mers.noMT.bwa.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.17/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa LS115_Li3-CRR995082.read1.paired.fastq.gz LS115_Li3-CRR995082.read2.paired.fastq.gz | egrep -v MT | ~/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa - |  ~/programs/samtools-0.1.18/samtools sort - LS115_Li3-CRR995082.2x36mers.noMT.bwa.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.17/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa LS115_Mu1-CRR995083.read1.paired.fastq.gz LS115_Mu1-CRR995083.read2.paired.fastq.gz | egrep -v MT | ~/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa - |  ~/programs/samtools-0.1.18/samtools sort - LS115_Mu1-CRR995083.2x36mers.noMT.bwa.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.17/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa LS115_Mu2-CRR995084.read1.paired.fastq.gz LS115_Mu2-CRR995084.read2.paired.fastq.gz | egrep -v MT | ~/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa - |  ~/programs/samtools-0.1.18/samtools sort - LS115_Mu2-CRR995084.2x36mers.noMT.bwa.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.17/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa LS115_Mu3-CRR995085.read1.paired.fastq.gz LS115_Mu3-CRR995085.read2.paired.fastq.gz | egrep -v MT | ~/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa - |  ~/programs/samtools-0.1.18/samtools sort - LS115_Mu3-CRR995085.2x36mers.noMT.bwa.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.17/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa LS168_B_Li1-CRR995087.read1.paired.fastq.gz LS168_B_Li1-CRR995087.read2.paired.fastq.gz | egrep -v MT | ~/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa - |  ~/programs/samtools-0.1.18/samtools sort - LS168_B_Li1-CRR995087.2x36mers.noMT.bwa.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.17/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa LS168_B_Mu1-CRR995088.read1.paired.fastq.gz LS168_B_Mu1-CRR995088.read2.paired.fastq.gz | egrep -v MT | ~/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa - |  ~/programs/samtools-0.1.18/samtools sort - LS168_B_Mu1-CRR995088.2x36mers.noMT.bwa.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.17/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa LS168_C_Br2-CRR995089.read1.paired.fastq.gz LS168_C_Br2-CRR995089.read2.paired.fastq.gz | egrep -v MT | ~/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa - |  ~/programs/samtools-0.1.18/samtools sort - LS168_C_Br2-CRR995089.2x36mers.noMT.bwa.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.17/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa LS168_C_Li2-CRR995090.read1.paired.fastq.gz LS168_C_Li2-CRR995090.read2.paired.fastq.gz | egrep -v MT | ~/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa - |  ~/programs/samtools-0.1.18/samtools sort - LS168_C_Li2-CRR995090.2x36mers.noMT.bwa.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.17/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa LS168_C_Mu2-CRR995091.read1.paired.fastq.gz LS168_C_Mu2-CRR995091.read2.paired.fastq.gz | egrep -v MT | ~/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa - |  ~/programs/samtools-0.1.18/samtools sort - LS168_C_Mu2-CRR995091.2x36mers.noMT.bwa.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.17/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa LS168_L_Li3-CRR995092.read1.paired.fastq.gz LS168_L_Li3-CRR995092.read2.paired.fastq.gz | egrep -v MT | ~/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa - |  ~/programs/samtools-0.1.18/samtools sort - LS168_L_Li3-CRR995092.2x36mers.noMT.bwa.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.17/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa LS40_Br2-CRR995095.read1.paired.fastq.gz LS40_Br2-CRR995095.read2.paired.fastq.gz | egrep -v MT | ~/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa - |  ~/programs/samtools-0.1.18/samtools sort - LS40_Br2-CRR995095.2x36mers.noMT.bwa.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.17/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa LS40_Br3-CRR995096.read1.paired.fastq.gz LS40_Br3-CRR995096.read2.paired.fastq.gz | egrep -v MT | ~/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa - |  ~/programs/samtools-0.1.18/samtools sort - LS40_Br3-CRR995096.2x36mers.noMT.bwa.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.17/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa LS40_Li1-CRR995097.read1.paired.fastq.gz LS40_Li1-CRR995097.read2.paired.fastq.gz | egrep -v MT | ~/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa - |  ~/programs/samtools-0.1.18/samtools sort - LS40_Li1-CRR995097.2x36mers.noMT.bwa.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.17/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa LS40_Li2-CRR995098.read1.paired.fastq.gz LS40_Li2-CRR995098.read2.paired.fastq.gz | egrep -v MT | ~/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa - |  ~/programs/samtools-0.1.18/samtools sort - LS40_Li2-CRR995098.2x36mers.noMT.bwa.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.17/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa LS40_Li3-CRR995099.read1.paired.fastq.gz LS40_Li3-CRR995099.read2.paired.fastq.gz | egrep -v MT | ~/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa - |  ~/programs/samtools-0.1.18/samtools sort - LS40_Li3-CRR995099.2x36mers.noMT.bwa.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.17/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa LS40_Mu1-CRR995100.read1.paired.fastq.gz LS40_Mu1-CRR995100.read2.paired.fastq.gz | egrep -v MT | ~/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa - |  ~/programs/samtools-0.1.18/samtools sort - LS40_Mu1-CRR995100.2x36mers.noMT.bwa.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.17/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa LS40_Mu2-CRR995101.read1.paired.fastq.gz LS40_Mu2-CRR995101.read2.paired.fastq.gz | egrep -v MT | ~/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa - |  ~/programs/samtools-0.1.18/samtools sort - LS40_Mu2-CRR995101.2x36mers.noMT.bwa.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.17/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa LS40_Mu3-CRR995102.read1.paired.fastq.gz LS40_Mu3-CRR995102.read2.paired.fastq.gz | egrep -v MT | ~/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa - |  ~/programs/samtools-0.1.18/samtools sort - LS40_Mu3-CRR995102.2x36mers.noMT.bwa.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.17/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa LS40_Pl1-CRR995103.read1.paired.fastq.gz LS40_Pl1-CRR995103.read2.paired.fastq.gz | egrep -v MT | ~/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa - |  ~/programs/samtools-0.1.18/samtools sort - LS40_Pl1-CRR995103.2x36mers.noMT.bwa.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.17/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa LS40_Pl2-CRR995104.read1.paired.fastq.gz LS40_Pl2-CRR995104.read2.paired.fastq.gz | egrep -v MT | ~/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa - |  ~/programs/samtools-0.1.18/samtools sort - LS40_Pl2-CRR995104.2x36mers.noMT.bwa.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.17/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa LS40_Pl3-CRR995105.read1.paired.fastq.gz LS40_Pl3-CRR995105.read2.paired.fastq.gz | egrep -v MT | ~/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa - |  ~/programs/samtools-0.1.18/samtools sort - LS40_Pl3-CRR995105.2x36mers.noMT.bwa.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.17/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa LS70_Br1-CRR995106.read1.paired.fastq.gz LS70_Br1-CRR995106.read2.paired.fastq.gz | egrep -v MT | ~/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa - |  ~/programs/samtools-0.1.18/samtools sort - LS70_Br1-CRR995106.2x36mers.noMT.bwa.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.17/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa LS70_Br2-CRR995107.read1.paired.fastq.gz LS70_Br2-CRR995107.read2.paired.fastq.gz | egrep -v MT | ~/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa - |  ~/programs/samtools-0.1.18/samtools sort - LS70_Br2-CRR995107.2x36mers.noMT.bwa.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.17/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa LS70_Br3-CRR995108.read1.paired.fastq.gz LS70_Br3-CRR995108.read2.paired.fastq.gz | egrep -v MT | ~/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa - |  ~/programs/samtools-0.1.18/samtools sort - LS70_Br3-CRR995108.2x36mers.noMT.bwa.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.17/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa LS70_Li1-CRR995109.read1.paired.fastq.gz LS70_Li1-CRR995109.read2.paired.fastq.gz | egrep -v MT | ~/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa - |  ~/programs/samtools-0.1.18/samtools sort - LS70_Li1-CRR995109.2x36mers.noMT.bwa.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.17/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa LS70_Li2-CRR995110.read1.paired.fastq.gz LS70_Li2-CRR995110.read2.paired.fastq.gz | egrep -v MT | ~/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa - |  ~/programs/samtools-0.1.18/samtools sort - LS70_Li2-CRR995110.2x36mers.noMT.bwa.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.17/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa LS70_Li3-CRR995111.read1.paired.fastq.gz LS70_Li3-CRR995111.read2.paired.fastq.gz | egrep -v MT | ~/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa - |  ~/programs/samtools-0.1.18/samtools sort - LS70_Li3-CRR995111.2x36mers.noMT.bwa.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.17/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa LS70_Mu1-CRR995112.read1.paired.fastq.gz LS70_Mu1-CRR995112.read2.paired.fastq.gz | egrep -v MT | ~/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa - |  ~/programs/samtools-0.1.18/samtools sort - LS70_Mu1-CRR995112.2x36mers.noMT.bwa.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.17/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa LS70_Mu2-CRR995113.read1.paired.fastq.gz LS70_Mu2-CRR995113.read2.paired.fastq.gz | egrep -v MT | ~/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa - |  ~/programs/samtools-0.1.18/samtools sort - LS70_Mu2-CRR995113.2x36mers.noMT.bwa.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.17/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa LS70_Mu3-CRR995114.read1.paired.fastq.gz LS70_Mu3-CRR995114.read2.paired.fastq.gz | egrep -v MT | ~/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa - |  ~/programs/samtools-0.1.18/samtools sort - LS70_Mu3-CRR995114.2x36mers.noMT.bwa.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.17/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa LS70_Pl2-CRR995115.read1.paired.fastq.gz LS70_Pl2-CRR995115.read2.paired.fastq.gz | egrep -v MT | ~/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa - |  ~/programs/samtools-0.1.18/samtools sort - LS70_Pl2-CRR995115.2x36mers.noMT.bwa.unique
/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.17/bwa mem -t 20 -M /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa LS70_Pl3-CRR995116.read1.paired.fastq.gz LS70_Pl3-CRR995116.read2.paired.fastq.gz | egrep -v MT | ~/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bwa-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa - |  ~/programs/samtools-0.1.18/samtools sort - LS70_Pl3-CRR995116.2x36mers.noMT.bwa.unique