python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py DB115_Br2-CRR994956.2x36mers.noMT.bwa.unique.dedup.bam SAMstats-DB115_Br2-CRR994956.2x36mers.noMT.bwa.unique.dedup -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py DB115_Br3-CRR994957.2x36mers.noMT.bwa.unique.dedup.bam SAMstats-DB115_Br3-CRR994957.2x36mers.noMT.bwa.unique.dedup -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py DB115_Li2-CRR994959.2x36mers.noMT.bwa.unique.dedup.bam SAMstats-DB115_Li2-CRR994959.2x36mers.noMT.bwa.unique.dedup -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py DB115_Li3-CRR994960.2x36mers.noMT.bwa.unique.dedup.bam SAMstats-DB115_Li3-CRR994960.2x36mers.noMT.bwa.unique.dedup -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py DB115_Mu1-CRR994961.2x36mers.noMT.bwa.unique.dedup.bam SAMstats-DB115_Mu1-CRR994961.2x36mers.noMT.bwa.unique.dedup -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py DB115_Mu2-CRR994962.2x36mers.noMT.bwa.unique.dedup.bam SAMstats-DB115_Mu2-CRR994962.2x36mers.noMT.bwa.unique.dedup -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py DB115_Mu3-CRR994963.2x36mers.noMT.bwa.unique.dedup.bam SAMstats-DB115_Mu3-CRR994963.2x36mers.noMT.bwa.unique.dedup -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py DB168_E_Br1-CRR994964.2x36mers.noMT.bwa.unique.dedup.bam SAMstats-DB168_E_Br1-CRR994964.2x36mers.noMT.bwa.unique.dedup -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py DB168_E_Li1-CRR994965.2x36mers.noMT.bwa.unique.dedup.bam SAMstats-DB168_E_Li1-CRR994965.2x36mers.noMT.bwa.unique.dedup -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py DB168_I_Br2-CRR994967.2x36mers.noMT.bwa.unique.dedup.bam SAMstats-DB168_I_Br2-CRR994967.2x36mers.noMT.bwa.unique.dedup -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py DB168_I_Li2-CRR994968.2x36mers.noMT.bwa.unique.dedup.bam SAMstats-DB168_I_Li2-CRR994968.2x36mers.noMT.bwa.unique.dedup -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py DB168_I_Mu2-CRR994969.2x36mers.noMT.bwa.unique.dedup.bam SAMstats-DB168_I_Mu2-CRR994969.2x36mers.noMT.bwa.unique.dedup -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py DB168_J_Br3-CRR994970.2x36mers.noMT.bwa.unique.dedup.bam SAMstats-DB168_J_Br3-CRR994970.2x36mers.noMT.bwa.unique.dedup -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py DB168_J_Li3-CRR994971.2x36mers.noMT.bwa.unique.dedup.bam SAMstats-DB168_J_Li3-CRR994971.2x36mers.noMT.bwa.unique.dedup -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py DB168_J_Mu3-CRR994972.2x36mers.noMT.bwa.unique.dedup.bam SAMstats-DB168_J_Mu3-CRR994972.2x36mers.noMT.bwa.unique.dedup -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py DB40_Br1-CRR994973.2x36mers.noMT.bwa.unique.dedup.bam SAMstats-DB40_Br1-CRR994973.2x36mers.noMT.bwa.unique.dedup -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py DB40_Li1-CRR994976.2x36mers.noMT.bwa.unique.dedup.bam SAMstats-DB40_Li1-CRR994976.2x36mers.noMT.bwa.unique.dedup -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py DB40_Li2-CRR994977.2x36mers.noMT.bwa.unique.dedup.bam SAMstats-DB40_Li2-CRR994977.2x36mers.noMT.bwa.unique.dedup -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py DB40_Li3-CRR994978.2x36mers.noMT.bwa.unique.dedup.bam SAMstats-DB40_Li3-CRR994978.2x36mers.noMT.bwa.unique.dedup -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py DB40_Mu1-CRR994979.2x36mers.noMT.bwa.unique.dedup.bam SAMstats-DB40_Mu1-CRR994979.2x36mers.noMT.bwa.unique.dedup -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py DB40_Mu2-CRR994980.2x36mers.noMT.bwa.unique.dedup.bam SAMstats-DB40_Mu2-CRR994980.2x36mers.noMT.bwa.unique.dedup -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py DB40_Mu3-CRR994981.2x36mers.noMT.bwa.unique.dedup.bam SAMstats-DB40_Mu3-CRR994981.2x36mers.noMT.bwa.unique.dedup -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py DB40_Pl1-CRR994982.2x36mers.noMT.bwa.unique.dedup.bam SAMstats-DB40_Pl1-CRR994982.2x36mers.noMT.bwa.unique.dedup -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py DB40_Pl2-CRR994983.2x36mers.noMT.bwa.unique.dedup.bam SAMstats-DB40_Pl2-CRR994983.2x36mers.noMT.bwa.unique.dedup -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py DB40_Pl3-CRR994984.2x36mers.noMT.bwa.unique.dedup.bam SAMstats-DB40_Pl3-CRR994984.2x36mers.noMT.bwa.unique.dedup -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py DB70_Br1-CRR994985.2x36mers.noMT.bwa.unique.dedup.bam SAMstats-DB70_Br1-CRR994985.2x36mers.noMT.bwa.unique.dedup -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py DB70_Br3-CRR994987.2x36mers.noMT.bwa.unique.dedup.bam SAMstats-DB70_Br3-CRR994987.2x36mers.noMT.bwa.unique.dedup -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py DB70_Li2-CRR994989.2x36mers.noMT.bwa.unique.dedup.bam SAMstats-DB70_Li2-CRR994989.2x36mers.noMT.bwa.unique.dedup -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py DB70_Li3-CRR994990.2x36mers.noMT.bwa.unique.dedup.bam SAMstats-DB70_Li3-CRR994990.2x36mers.noMT.bwa.unique.dedup -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py DB70_Mu1-CRR994991.2x36mers.noMT.bwa.unique.dedup.bam SAMstats-DB70_Mu1-CRR994991.2x36mers.noMT.bwa.unique.dedup -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py DB70_Mu2-CRR994992.2x36mers.noMT.bwa.unique.dedup.bam SAMstats-DB70_Mu2-CRR994992.2x36mers.noMT.bwa.unique.dedup -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py DB70_Mu3-CRR994993.2x36mers.noMT.bwa.unique.dedup.bam SAMstats-DB70_Mu3-CRR994993.2x36mers.noMT.bwa.unique.dedup -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py DB70_Pl1-CRR994994.2x36mers.noMT.bwa.unique.dedup.bam SAMstats-DB70_Pl1-CRR994994.2x36mers.noMT.bwa.unique.dedup -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py DS115_Br1-CRR994995.2x36mers.noMT.bwa.unique.dedup.bam SAMstats-DS115_Br1-CRR994995.2x36mers.noMT.bwa.unique.dedup -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py DS115_Br2-CRR994996.2x36mers.noMT.bwa.unique.dedup.bam SAMstats-DS115_Br2-CRR994996.2x36mers.noMT.bwa.unique.dedup -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py DS115_Br3-CRR994997.2x36mers.noMT.bwa.unique.dedup.bam SAMstats-DS115_Br3-CRR994997.2x36mers.noMT.bwa.unique.dedup -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py DS115_Li1-CRR994998.2x36mers.noMT.bwa.unique.dedup.bam SAMstats-DS115_Li1-CRR994998.2x36mers.noMT.bwa.unique.dedup -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py DS115_Li2-CRR994999.2x36mers.noMT.bwa.unique.dedup.bam SAMstats-DS115_Li2-CRR994999.2x36mers.noMT.bwa.unique.dedup -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py DS115_Li3-CRR995000.2x36mers.noMT.bwa.unique.dedup.bam SAMstats-DS115_Li3-CRR995000.2x36mers.noMT.bwa.unique.dedup -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py DS115_Mu1-CRR995001.2x36mers.noMT.bwa.unique.dedup.bam SAMstats-DS115_Mu1-CRR995001.2x36mers.noMT.bwa.unique.dedup -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py DS115_Mu2-CRR995002.2x36mers.noMT.bwa.unique.dedup.bam SAMstats-DS115_Mu2-CRR995002.2x36mers.noMT.bwa.unique.dedup -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py DS115_Mu3-CRR995003.2x36mers.noMT.bwa.unique.dedup.bam SAMstats-DS115_Mu3-CRR995003.2x36mers.noMT.bwa.unique.dedup -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py DS168_M_Br1-CRR995004.2x36mers.noMT.bwa.unique.dedup.bam SAMstats-DS168_M_Br1-CRR995004.2x36mers.noMT.bwa.unique.dedup -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py DS168_M_Li1-CRR995005.2x36mers.noMT.bwa.unique.dedup.bam SAMstats-DS168_M_Li1-CRR995005.2x36mers.noMT.bwa.unique.dedup -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py DS168_N_Br2-CRR995007.2x36mers.noMT.bwa.unique.dedup.bam SAMstats-DS168_N_Br2-CRR995007.2x36mers.noMT.bwa.unique.dedup -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py DS168_N_Li2-CRR995008.2x36mers.noMT.bwa.unique.dedup.bam SAMstats-DS168_N_Li2-CRR995008.2x36mers.noMT.bwa.unique.dedup -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py DS168_N_Mu2-CRR995009.2x36mers.noMT.bwa.unique.dedup.bam SAMstats-DS168_N_Mu2-CRR995009.2x36mers.noMT.bwa.unique.dedup -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py DS168_O_Br3-CRR995010.2x36mers.noMT.bwa.unique.dedup.bam SAMstats-DS168_O_Br3-CRR995010.2x36mers.noMT.bwa.unique.dedup -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py DS168_O_Li3-CRR995011.2x36mers.noMT.bwa.unique.dedup.bam SAMstats-DS168_O_Li3-CRR995011.2x36mers.noMT.bwa.unique.dedup -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py DS40_Br1-CRR995013.2x36mers.noMT.bwa.unique.dedup.bam SAMstats-DS40_Br1-CRR995013.2x36mers.noMT.bwa.unique.dedup -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py DS40_Br2-CRR995014.2x36mers.noMT.bwa.unique.dedup.bam SAMstats-DS40_Br2-CRR995014.2x36mers.noMT.bwa.unique.dedup -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py DS40_Br3-CRR995015.2x36mers.noMT.bwa.unique.dedup.bam SAMstats-DS40_Br3-CRR995015.2x36mers.noMT.bwa.unique.dedup -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py DS40_Li2-CRR995016.2x36mers.noMT.bwa.unique.dedup.bam SAMstats-DS40_Li2-CRR995016.2x36mers.noMT.bwa.unique.dedup -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py DS40_Li3-CRR995017.2x36mers.noMT.bwa.unique.dedup.bam SAMstats-DS40_Li3-CRR995017.2x36mers.noMT.bwa.unique.dedup -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py DS40_Mu1-CRR995018.2x36mers.noMT.bwa.unique.dedup.bam SAMstats-DS40_Mu1-CRR995018.2x36mers.noMT.bwa.unique.dedup -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py DS40_Mu2-CRR995019.2x36mers.noMT.bwa.unique.dedup.bam SAMstats-DS40_Mu2-CRR995019.2x36mers.noMT.bwa.unique.dedup -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py DS40_Mu3-CRR995020.2x36mers.noMT.bwa.unique.dedup.bam SAMstats-DS40_Mu3-CRR995020.2x36mers.noMT.bwa.unique.dedup -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py DS40_Pl1-CRR995021.2x36mers.noMT.bwa.unique.dedup.bam SAMstats-DS40_Pl1-CRR995021.2x36mers.noMT.bwa.unique.dedup -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py DS40_Pl2-CRR995022.2x36mers.noMT.bwa.unique.dedup.bam SAMstats-DS40_Pl2-CRR995022.2x36mers.noMT.bwa.unique.dedup -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py DS40_Pl3-CRR995023.2x36mers.noMT.bwa.unique.dedup.bam SAMstats-DS40_Pl3-CRR995023.2x36mers.noMT.bwa.unique.dedup -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py DS70_Br1-CRR995024.2x36mers.noMT.bwa.unique.dedup.bam SAMstats-DS70_Br1-CRR995024.2x36mers.noMT.bwa.unique.dedup -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py DS70_Br2-CRR995025.2x36mers.noMT.bwa.unique.dedup.bam SAMstats-DS70_Br2-CRR995025.2x36mers.noMT.bwa.unique.dedup -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py DS70_Br3-CRR995026.2x36mers.noMT.bwa.unique.dedup.bam SAMstats-DS70_Br3-CRR995026.2x36mers.noMT.bwa.unique.dedup -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py DS70_Li1-CRR995027.2x36mers.noMT.bwa.unique.dedup.bam SAMstats-DS70_Li1-CRR995027.2x36mers.noMT.bwa.unique.dedup -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py DS70_Li2-CRR995028.2x36mers.noMT.bwa.unique.dedup.bam SAMstats-DS70_Li2-CRR995028.2x36mers.noMT.bwa.unique.dedup -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py DS70_Li3-CRR995029.2x36mers.noMT.bwa.unique.dedup.bam SAMstats-DS70_Li3-CRR995029.2x36mers.noMT.bwa.unique.dedup -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py DS70_Mu1-CRR995030.2x36mers.noMT.bwa.unique.dedup.bam SAMstats-DS70_Mu1-CRR995030.2x36mers.noMT.bwa.unique.dedup -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py DS70_Mu2-CRR995031.2x36mers.noMT.bwa.unique.dedup.bam SAMstats-DS70_Mu2-CRR995031.2x36mers.noMT.bwa.unique.dedup -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py DS70_Mu3-CRR995032.2x36mers.noMT.bwa.unique.dedup.bam SAMstats-DS70_Mu3-CRR995032.2x36mers.noMT.bwa.unique.dedup -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py DS70_Pl1-CRR995033.2x36mers.noMT.bwa.unique.dedup.bam SAMstats-DS70_Pl1-CRR995033.2x36mers.noMT.bwa.unique.dedup -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py DS70_Pl3-CRR995034.2x36mers.noMT.bwa.unique.dedup.bam SAMstats-DS70_Pl3-CRR995034.2x36mers.noMT.bwa.unique.dedup -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py LB115_Br1-CRR995035.2x36mers.noMT.bwa.unique.dedup.bam SAMstats-LB115_Br1-CRR995035.2x36mers.noMT.bwa.unique.dedup -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py LB115_Br2-CRR995036.2x36mers.noMT.bwa.unique.dedup.bam SAMstats-LB115_Br2-CRR995036.2x36mers.noMT.bwa.unique.dedup -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py LB115_Br3-CRR995037.2x36mers.noMT.bwa.unique.dedup.bam SAMstats-LB115_Br3-CRR995037.2x36mers.noMT.bwa.unique.dedup -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py LB115_Li1-CRR995038.2x36mers.noMT.bwa.unique.dedup.bam SAMstats-LB115_Li1-CRR995038.2x36mers.noMT.bwa.unique.dedup -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py LB115_Li2-CRR995039.2x36mers.noMT.bwa.unique.dedup.bam SAMstats-LB115_Li2-CRR995039.2x36mers.noMT.bwa.unique.dedup -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py LB115_Li3-CRR995040.2x36mers.noMT.bwa.unique.dedup.bam SAMstats-LB115_Li3-CRR995040.2x36mers.noMT.bwa.unique.dedup -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py LB115_Mu1-CRR995041.2x36mers.noMT.bwa.unique.dedup.bam SAMstats-LB115_Mu1-CRR995041.2x36mers.noMT.bwa.unique.dedup -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py LB115_Mu2-CRR995042.2x36mers.noMT.bwa.unique.dedup.bam SAMstats-LB115_Mu2-CRR995042.2x36mers.noMT.bwa.unique.dedup -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py LB115_Mu3-CRR995043.2x36mers.noMT.bwa.unique.dedup.bam SAMstats-LB115_Mu3-CRR995043.2x36mers.noMT.bwa.unique.dedup -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py LB168_F_Br2-CRR995044.2x36mers.noMT.bwa.unique.dedup.bam SAMstats-LB168_F_Br2-CRR995044.2x36mers.noMT.bwa.unique.dedup -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py LB168_F_Li2-CRR995045.2x36mers.noMT.bwa.unique.dedup.bam SAMstats-LB168_F_Li2-CRR995045.2x36mers.noMT.bwa.unique.dedup -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py LB168_F_Mu2-CRR995046.2x36mers.noMT.bwa.unique.dedup.bam SAMstats-LB168_F_Mu2-CRR995046.2x36mers.noMT.bwa.unique.dedup -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py LB168_G_Br1-CRR995047.2x36mers.noMT.bwa.unique.dedup.bam SAMstats-LB168_G_Br1-CRR995047.2x36mers.noMT.bwa.unique.dedup -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py LB168_G_Li1-CRR995048.2x36mers.noMT.bwa.unique.dedup.bam SAMstats-LB168_G_Li1-CRR995048.2x36mers.noMT.bwa.unique.dedup -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py LB168_G_Mu1-CRR995049.2x36mers.noMT.bwa.unique.dedup.bam SAMstats-LB168_G_Mu1-CRR995049.2x36mers.noMT.bwa.unique.dedup -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py LB168_H_Br3-CRR995050.2x36mers.noMT.bwa.unique.dedup.bam SAMstats-LB168_H_Br3-CRR995050.2x36mers.noMT.bwa.unique.dedup -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py LB168_H_Li3-CRR995051.2x36mers.noMT.bwa.unique.dedup.bam SAMstats-LB168_H_Li3-CRR995051.2x36mers.noMT.bwa.unique.dedup -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py LB168_H_Mu3-CRR995052.2x36mers.noMT.bwa.unique.dedup.bam SAMstats-LB168_H_Mu3-CRR995052.2x36mers.noMT.bwa.unique.dedup -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py LB40_Br1-CRR995053.2x36mers.noMT.bwa.unique.dedup.bam SAMstats-LB40_Br1-CRR995053.2x36mers.noMT.bwa.unique.dedup -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py LB40_Br3-CRR995055.2x36mers.noMT.bwa.unique.dedup.bam SAMstats-LB40_Br3-CRR995055.2x36mers.noMT.bwa.unique.dedup -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py LB40_Li1-CRR995056.2x36mers.noMT.bwa.unique.dedup.bam SAMstats-LB40_Li1-CRR995056.2x36mers.noMT.bwa.unique.dedup -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py LB40_Li2-CRR995057.2x36mers.noMT.bwa.unique.dedup.bam SAMstats-LB40_Li2-CRR995057.2x36mers.noMT.bwa.unique.dedup -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py LB40_Li3-CRR995058.2x36mers.noMT.bwa.unique.dedup.bam SAMstats-LB40_Li3-CRR995058.2x36mers.noMT.bwa.unique.dedup -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py LB40_Mu2-CRR995060.2x36mers.noMT.bwa.unique.dedup.bam SAMstats-LB40_Mu2-CRR995060.2x36mers.noMT.bwa.unique.dedup -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py LB40_Mu3-CRR995061.2x36mers.noMT.bwa.unique.dedup.bam SAMstats-LB40_Mu3-CRR995061.2x36mers.noMT.bwa.unique.dedup -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py LB40_Pl1-CRR995062.2x36mers.noMT.bwa.unique.dedup.bam SAMstats-LB40_Pl1-CRR995062.2x36mers.noMT.bwa.unique.dedup -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py LB40_Pl2-CRR995063.2x36mers.noMT.bwa.unique.dedup.bam SAMstats-LB40_Pl2-CRR995063.2x36mers.noMT.bwa.unique.dedup -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py LB40_Pl3-CRR995064.2x36mers.noMT.bwa.unique.dedup.bam SAMstats-LB40_Pl3-CRR995064.2x36mers.noMT.bwa.unique.dedup -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py LB70_Br1-CRR995065.2x36mers.noMT.bwa.unique.dedup.bam SAMstats-LB70_Br1-CRR995065.2x36mers.noMT.bwa.unique.dedup -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py LB70_Br2-CRR995066.2x36mers.noMT.bwa.unique.dedup.bam SAMstats-LB70_Br2-CRR995066.2x36mers.noMT.bwa.unique.dedup -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py LB70_Br3-CRR995067.2x36mers.noMT.bwa.unique.dedup.bam SAMstats-LB70_Br3-CRR995067.2x36mers.noMT.bwa.unique.dedup -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py LB70_Li1-CRR995068.2x36mers.noMT.bwa.unique.dedup.bam SAMstats-LB70_Li1-CRR995068.2x36mers.noMT.bwa.unique.dedup -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py LB70_Li2-CRR995069.2x36mers.noMT.bwa.unique.dedup.bam SAMstats-LB70_Li2-CRR995069.2x36mers.noMT.bwa.unique.dedup -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py LB70_Li3-CRR995070.2x36mers.noMT.bwa.unique.dedup.bam SAMstats-LB70_Li3-CRR995070.2x36mers.noMT.bwa.unique.dedup -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py LB70_Mu1-CRR995071.2x36mers.noMT.bwa.unique.dedup.bam SAMstats-LB70_Mu1-CRR995071.2x36mers.noMT.bwa.unique.dedup -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py LB70_Mu2-CRR995072.2x36mers.noMT.bwa.unique.dedup.bam SAMstats-LB70_Mu2-CRR995072.2x36mers.noMT.bwa.unique.dedup -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py LB70_Mu3-CRR995073.2x36mers.noMT.bwa.unique.dedup.bam SAMstats-LB70_Mu3-CRR995073.2x36mers.noMT.bwa.unique.dedup -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py LB70_Pl1-CRR995074.2x36mers.noMT.bwa.unique.dedup.bam SAMstats-LB70_Pl1-CRR995074.2x36mers.noMT.bwa.unique.dedup -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py LB70_Pl2-CRR995075.2x36mers.noMT.bwa.unique.dedup.bam SAMstats-LB70_Pl2-CRR995075.2x36mers.noMT.bwa.unique.dedup -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py LB70_Pl3-CRR995076.2x36mers.noMT.bwa.unique.dedup.bam SAMstats-LB70_Pl3-CRR995076.2x36mers.noMT.bwa.unique.dedup -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py LS115_Br1-CRR995077.2x36mers.noMT.bwa.unique.dedup.bam SAMstats-LS115_Br1-CRR995077.2x36mers.noMT.bwa.unique.dedup -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py LS115_Br2-CRR995078.2x36mers.noMT.bwa.unique.dedup.bam SAMstats-LS115_Br2-CRR995078.2x36mers.noMT.bwa.unique.dedup -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py LS115_Br3-CRR995079.2x36mers.noMT.bwa.unique.dedup.bam SAMstats-LS115_Br3-CRR995079.2x36mers.noMT.bwa.unique.dedup -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py LS115_Li1-CRR995080.2x36mers.noMT.bwa.unique.dedup.bam SAMstats-LS115_Li1-CRR995080.2x36mers.noMT.bwa.unique.dedup -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py LS115_Li2-CRR995081.2x36mers.noMT.bwa.unique.dedup.bam SAMstats-LS115_Li2-CRR995081.2x36mers.noMT.bwa.unique.dedup -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py LS115_Li3-CRR995082.2x36mers.noMT.bwa.unique.dedup.bam SAMstats-LS115_Li3-CRR995082.2x36mers.noMT.bwa.unique.dedup -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py LS115_Mu1-CRR995083.2x36mers.noMT.bwa.unique.dedup.bam SAMstats-LS115_Mu1-CRR995083.2x36mers.noMT.bwa.unique.dedup -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py LS115_Mu2-CRR995084.2x36mers.noMT.bwa.unique.dedup.bam SAMstats-LS115_Mu2-CRR995084.2x36mers.noMT.bwa.unique.dedup -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py LS115_Mu3-CRR995085.2x36mers.noMT.bwa.unique.dedup.bam SAMstats-LS115_Mu3-CRR995085.2x36mers.noMT.bwa.unique.dedup -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py LS168_B_Li1-CRR995087.2x36mers.noMT.bwa.unique.dedup.bam SAMstats-LS168_B_Li1-CRR995087.2x36mers.noMT.bwa.unique.dedup -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py LS168_B_Mu1-CRR995088.2x36mers.noMT.bwa.unique.dedup.bam SAMstats-LS168_B_Mu1-CRR995088.2x36mers.noMT.bwa.unique.dedup -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py LS168_C_Br2-CRR995089.2x36mers.noMT.bwa.unique.dedup.bam SAMstats-LS168_C_Br2-CRR995089.2x36mers.noMT.bwa.unique.dedup -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py LS168_C_Li2-CRR995090.2x36mers.noMT.bwa.unique.dedup.bam SAMstats-LS168_C_Li2-CRR995090.2x36mers.noMT.bwa.unique.dedup -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py LS168_C_Mu2-CRR995091.2x36mers.noMT.bwa.unique.dedup.bam SAMstats-LS168_C_Mu2-CRR995091.2x36mers.noMT.bwa.unique.dedup -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py LS168_L_Li3-CRR995092.2x36mers.noMT.bwa.unique.dedup.bam SAMstats-LS168_L_Li3-CRR995092.2x36mers.noMT.bwa.unique.dedup -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py LS40_Br2-CRR995095.2x36mers.noMT.bwa.unique.dedup.bam SAMstats-LS40_Br2-CRR995095.2x36mers.noMT.bwa.unique.dedup -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py LS40_Br3-CRR995096.2x36mers.noMT.bwa.unique.dedup.bam SAMstats-LS40_Br3-CRR995096.2x36mers.noMT.bwa.unique.dedup -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py LS40_Li1-CRR995097.2x36mers.noMT.bwa.unique.dedup.bam SAMstats-LS40_Li1-CRR995097.2x36mers.noMT.bwa.unique.dedup -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py LS40_Li2-CRR995098.2x36mers.noMT.bwa.unique.dedup.bam SAMstats-LS40_Li2-CRR995098.2x36mers.noMT.bwa.unique.dedup -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py LS40_Li3-CRR995099.2x36mers.noMT.bwa.unique.dedup.bam SAMstats-LS40_Li3-CRR995099.2x36mers.noMT.bwa.unique.dedup -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py LS40_Mu1-CRR995100.2x36mers.noMT.bwa.unique.dedup.bam SAMstats-LS40_Mu1-CRR995100.2x36mers.noMT.bwa.unique.dedup -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py LS40_Mu2-CRR995101.2x36mers.noMT.bwa.unique.dedup.bam SAMstats-LS40_Mu2-CRR995101.2x36mers.noMT.bwa.unique.dedup -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py LS40_Mu3-CRR995102.2x36mers.noMT.bwa.unique.dedup.bam SAMstats-LS40_Mu3-CRR995102.2x36mers.noMT.bwa.unique.dedup -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py LS40_Pl1-CRR995103.2x36mers.noMT.bwa.unique.dedup.bam SAMstats-LS40_Pl1-CRR995103.2x36mers.noMT.bwa.unique.dedup -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py LS40_Pl2-CRR995104.2x36mers.noMT.bwa.unique.dedup.bam SAMstats-LS40_Pl2-CRR995104.2x36mers.noMT.bwa.unique.dedup -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py LS40_Pl3-CRR995105.2x36mers.noMT.bwa.unique.dedup.bam SAMstats-LS40_Pl3-CRR995105.2x36mers.noMT.bwa.unique.dedup -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py LS70_Br1-CRR995106.2x36mers.noMT.bwa.unique.dedup.bam SAMstats-LS70_Br1-CRR995106.2x36mers.noMT.bwa.unique.dedup -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py LS70_Br2-CRR995107.2x36mers.noMT.bwa.unique.dedup.bam SAMstats-LS70_Br2-CRR995107.2x36mers.noMT.bwa.unique.dedup -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py LS70_Br3-CRR995108.2x36mers.noMT.bwa.unique.dedup.bam SAMstats-LS70_Br3-CRR995108.2x36mers.noMT.bwa.unique.dedup -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py LS70_Li1-CRR995109.2x36mers.noMT.bwa.unique.dedup.bam SAMstats-LS70_Li1-CRR995109.2x36mers.noMT.bwa.unique.dedup -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py LS70_Li2-CRR995110.2x36mers.noMT.bwa.unique.dedup.bam SAMstats-LS70_Li2-CRR995110.2x36mers.noMT.bwa.unique.dedup -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py LS70_Li3-CRR995111.2x36mers.noMT.bwa.unique.dedup.bam SAMstats-LS70_Li3-CRR995111.2x36mers.noMT.bwa.unique.dedup -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py LS70_Mu1-CRR995112.2x36mers.noMT.bwa.unique.dedup.bam SAMstats-LS70_Mu1-CRR995112.2x36mers.noMT.bwa.unique.dedup -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py LS70_Mu2-CRR995113.2x36mers.noMT.bwa.unique.dedup.bam SAMstats-LS70_Mu2-CRR995113.2x36mers.noMT.bwa.unique.dedup -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py LS70_Mu3-CRR995114.2x36mers.noMT.bwa.unique.dedup.bam SAMstats-LS70_Mu3-CRR995114.2x36mers.noMT.bwa.unique.dedup -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py LS70_Pl2-CRR995115.2x36mers.noMT.bwa.unique.dedup.bam SAMstats-LS70_Pl2-CRR995115.2x36mers.noMT.bwa.unique.dedup -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py LS70_Pl3-CRR995116.2x36mers.noMT.bwa.unique.dedup.bam SAMstats-LS70_Pl3-CRR995116.2x36mers.noMT.bwa.unique.dedup -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py DB115_Br2-CRR994956.2x36mers.noMT.bwa.unique.bam SAMstats-DB115_Br2-CRR994956.2x36mers.noMT.bwa.unique -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py DB115_Br3-CRR994957.2x36mers.noMT.bwa.unique.bam SAMstats-DB115_Br3-CRR994957.2x36mers.noMT.bwa.unique -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py DB115_Li2-CRR994959.2x36mers.noMT.bwa.unique.bam SAMstats-DB115_Li2-CRR994959.2x36mers.noMT.bwa.unique -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py DB115_Li3-CRR994960.2x36mers.noMT.bwa.unique.bam SAMstats-DB115_Li3-CRR994960.2x36mers.noMT.bwa.unique -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py DB115_Mu1-CRR994961.2x36mers.noMT.bwa.unique.bam SAMstats-DB115_Mu1-CRR994961.2x36mers.noMT.bwa.unique -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py DB115_Mu2-CRR994962.2x36mers.noMT.bwa.unique.bam SAMstats-DB115_Mu2-CRR994962.2x36mers.noMT.bwa.unique -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py DB115_Mu3-CRR994963.2x36mers.noMT.bwa.unique.bam SAMstats-DB115_Mu3-CRR994963.2x36mers.noMT.bwa.unique -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py DB168_E_Br1-CRR994964.2x36mers.noMT.bwa.unique.bam SAMstats-DB168_E_Br1-CRR994964.2x36mers.noMT.bwa.unique -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py DB168_E_Li1-CRR994965.2x36mers.noMT.bwa.unique.bam SAMstats-DB168_E_Li1-CRR994965.2x36mers.noMT.bwa.unique -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py DB168_I_Br2-CRR994967.2x36mers.noMT.bwa.unique.bam SAMstats-DB168_I_Br2-CRR994967.2x36mers.noMT.bwa.unique -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py DB168_I_Li2-CRR994968.2x36mers.noMT.bwa.unique.bam SAMstats-DB168_I_Li2-CRR994968.2x36mers.noMT.bwa.unique -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py DB168_I_Mu2-CRR994969.2x36mers.noMT.bwa.unique.bam SAMstats-DB168_I_Mu2-CRR994969.2x36mers.noMT.bwa.unique -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py DB168_J_Br3-CRR994970.2x36mers.noMT.bwa.unique.bam SAMstats-DB168_J_Br3-CRR994970.2x36mers.noMT.bwa.unique -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py DB168_J_Li3-CRR994971.2x36mers.noMT.bwa.unique.bam SAMstats-DB168_J_Li3-CRR994971.2x36mers.noMT.bwa.unique -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py DB168_J_Mu3-CRR994972.2x36mers.noMT.bwa.unique.bam SAMstats-DB168_J_Mu3-CRR994972.2x36mers.noMT.bwa.unique -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py DB40_Br1-CRR994973.2x36mers.noMT.bwa.unique.bam SAMstats-DB40_Br1-CRR994973.2x36mers.noMT.bwa.unique -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py DB40_Li1-CRR994976.2x36mers.noMT.bwa.unique.bam SAMstats-DB40_Li1-CRR994976.2x36mers.noMT.bwa.unique -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py DB40_Li2-CRR994977.2x36mers.noMT.bwa.unique.bam SAMstats-DB40_Li2-CRR994977.2x36mers.noMT.bwa.unique -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py DB40_Li3-CRR994978.2x36mers.noMT.bwa.unique.bam SAMstats-DB40_Li3-CRR994978.2x36mers.noMT.bwa.unique -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py DB40_Mu1-CRR994979.2x36mers.noMT.bwa.unique.bam SAMstats-DB40_Mu1-CRR994979.2x36mers.noMT.bwa.unique -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py DB40_Mu2-CRR994980.2x36mers.noMT.bwa.unique.bam SAMstats-DB40_Mu2-CRR994980.2x36mers.noMT.bwa.unique -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py DB40_Mu3-CRR994981.2x36mers.noMT.bwa.unique.bam SAMstats-DB40_Mu3-CRR994981.2x36mers.noMT.bwa.unique -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py DB40_Pl1-CRR994982.2x36mers.noMT.bwa.unique.bam SAMstats-DB40_Pl1-CRR994982.2x36mers.noMT.bwa.unique -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py DB40_Pl2-CRR994983.2x36mers.noMT.bwa.unique.bam SAMstats-DB40_Pl2-CRR994983.2x36mers.noMT.bwa.unique -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py DB40_Pl3-CRR994984.2x36mers.noMT.bwa.unique.bam SAMstats-DB40_Pl3-CRR994984.2x36mers.noMT.bwa.unique -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py DB70_Br1-CRR994985.2x36mers.noMT.bwa.unique.bam SAMstats-DB70_Br1-CRR994985.2x36mers.noMT.bwa.unique -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py DB70_Br3-CRR994987.2x36mers.noMT.bwa.unique.bam SAMstats-DB70_Br3-CRR994987.2x36mers.noMT.bwa.unique -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py DB70_Li2-CRR994989.2x36mers.noMT.bwa.unique.bam SAMstats-DB70_Li2-CRR994989.2x36mers.noMT.bwa.unique -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py DB70_Li3-CRR994990.2x36mers.noMT.bwa.unique.bam SAMstats-DB70_Li3-CRR994990.2x36mers.noMT.bwa.unique -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py DB70_Mu1-CRR994991.2x36mers.noMT.bwa.unique.bam SAMstats-DB70_Mu1-CRR994991.2x36mers.noMT.bwa.unique -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py DB70_Mu2-CRR994992.2x36mers.noMT.bwa.unique.bam SAMstats-DB70_Mu2-CRR994992.2x36mers.noMT.bwa.unique -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py DB70_Mu3-CRR994993.2x36mers.noMT.bwa.unique.bam SAMstats-DB70_Mu3-CRR994993.2x36mers.noMT.bwa.unique -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py DB70_Pl1-CRR994994.2x36mers.noMT.bwa.unique.bam SAMstats-DB70_Pl1-CRR994994.2x36mers.noMT.bwa.unique -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py DS115_Br1-CRR994995.2x36mers.noMT.bwa.unique.bam SAMstats-DS115_Br1-CRR994995.2x36mers.noMT.bwa.unique -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py DS115_Br2-CRR994996.2x36mers.noMT.bwa.unique.bam SAMstats-DS115_Br2-CRR994996.2x36mers.noMT.bwa.unique -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py DS115_Br3-CRR994997.2x36mers.noMT.bwa.unique.bam SAMstats-DS115_Br3-CRR994997.2x36mers.noMT.bwa.unique -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py DS115_Li1-CRR994998.2x36mers.noMT.bwa.unique.bam SAMstats-DS115_Li1-CRR994998.2x36mers.noMT.bwa.unique -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py DS115_Li2-CRR994999.2x36mers.noMT.bwa.unique.bam SAMstats-DS115_Li2-CRR994999.2x36mers.noMT.bwa.unique -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py DS115_Li3-CRR995000.2x36mers.noMT.bwa.unique.bam SAMstats-DS115_Li3-CRR995000.2x36mers.noMT.bwa.unique -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py DS115_Mu1-CRR995001.2x36mers.noMT.bwa.unique.bam SAMstats-DS115_Mu1-CRR995001.2x36mers.noMT.bwa.unique -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py DS115_Mu2-CRR995002.2x36mers.noMT.bwa.unique.bam SAMstats-DS115_Mu2-CRR995002.2x36mers.noMT.bwa.unique -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py DS115_Mu3-CRR995003.2x36mers.noMT.bwa.unique.bam SAMstats-DS115_Mu3-CRR995003.2x36mers.noMT.bwa.unique -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py DS168_M_Br1-CRR995004.2x36mers.noMT.bwa.unique.bam SAMstats-DS168_M_Br1-CRR995004.2x36mers.noMT.bwa.unique -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py DS168_M_Li1-CRR995005.2x36mers.noMT.bwa.unique.bam SAMstats-DS168_M_Li1-CRR995005.2x36mers.noMT.bwa.unique -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py DS168_N_Br2-CRR995007.2x36mers.noMT.bwa.unique.bam SAMstats-DS168_N_Br2-CRR995007.2x36mers.noMT.bwa.unique -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py DS168_N_Li2-CRR995008.2x36mers.noMT.bwa.unique.bam SAMstats-DS168_N_Li2-CRR995008.2x36mers.noMT.bwa.unique -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py DS168_N_Mu2-CRR995009.2x36mers.noMT.bwa.unique.bam SAMstats-DS168_N_Mu2-CRR995009.2x36mers.noMT.bwa.unique -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py DS168_O_Br3-CRR995010.2x36mers.noMT.bwa.unique.bam SAMstats-DS168_O_Br3-CRR995010.2x36mers.noMT.bwa.unique -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py DS168_O_Li3-CRR995011.2x36mers.noMT.bwa.unique.bam SAMstats-DS168_O_Li3-CRR995011.2x36mers.noMT.bwa.unique -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py DS40_Br1-CRR995013.2x36mers.noMT.bwa.unique.bam SAMstats-DS40_Br1-CRR995013.2x36mers.noMT.bwa.unique -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py DS40_Br2-CRR995014.2x36mers.noMT.bwa.unique.bam SAMstats-DS40_Br2-CRR995014.2x36mers.noMT.bwa.unique -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py DS40_Br3-CRR995015.2x36mers.noMT.bwa.unique.bam SAMstats-DS40_Br3-CRR995015.2x36mers.noMT.bwa.unique -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py DS40_Li2-CRR995016.2x36mers.noMT.bwa.unique.bam SAMstats-DS40_Li2-CRR995016.2x36mers.noMT.bwa.unique -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py DS40_Li3-CRR995017.2x36mers.noMT.bwa.unique.bam SAMstats-DS40_Li3-CRR995017.2x36mers.noMT.bwa.unique -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py DS40_Mu1-CRR995018.2x36mers.noMT.bwa.unique.bam SAMstats-DS40_Mu1-CRR995018.2x36mers.noMT.bwa.unique -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py DS40_Mu2-CRR995019.2x36mers.noMT.bwa.unique.bam SAMstats-DS40_Mu2-CRR995019.2x36mers.noMT.bwa.unique -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py DS40_Mu3-CRR995020.2x36mers.noMT.bwa.unique.bam SAMstats-DS40_Mu3-CRR995020.2x36mers.noMT.bwa.unique -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py DS40_Pl1-CRR995021.2x36mers.noMT.bwa.unique.bam SAMstats-DS40_Pl1-CRR995021.2x36mers.noMT.bwa.unique -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py DS40_Pl2-CRR995022.2x36mers.noMT.bwa.unique.bam SAMstats-DS40_Pl2-CRR995022.2x36mers.noMT.bwa.unique -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py DS40_Pl3-CRR995023.2x36mers.noMT.bwa.unique.bam SAMstats-DS40_Pl3-CRR995023.2x36mers.noMT.bwa.unique -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py DS70_Br1-CRR995024.2x36mers.noMT.bwa.unique.bam SAMstats-DS70_Br1-CRR995024.2x36mers.noMT.bwa.unique -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py DS70_Br2-CRR995025.2x36mers.noMT.bwa.unique.bam SAMstats-DS70_Br2-CRR995025.2x36mers.noMT.bwa.unique -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py DS70_Br3-CRR995026.2x36mers.noMT.bwa.unique.bam SAMstats-DS70_Br3-CRR995026.2x36mers.noMT.bwa.unique -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py DS70_Li1-CRR995027.2x36mers.noMT.bwa.unique.bam SAMstats-DS70_Li1-CRR995027.2x36mers.noMT.bwa.unique -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py DS70_Li2-CRR995028.2x36mers.noMT.bwa.unique.bam SAMstats-DS70_Li2-CRR995028.2x36mers.noMT.bwa.unique -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py DS70_Li3-CRR995029.2x36mers.noMT.bwa.unique.bam SAMstats-DS70_Li3-CRR995029.2x36mers.noMT.bwa.unique -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py DS70_Mu1-CRR995030.2x36mers.noMT.bwa.unique.bam SAMstats-DS70_Mu1-CRR995030.2x36mers.noMT.bwa.unique -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py DS70_Mu2-CRR995031.2x36mers.noMT.bwa.unique.bam SAMstats-DS70_Mu2-CRR995031.2x36mers.noMT.bwa.unique -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py DS70_Mu3-CRR995032.2x36mers.noMT.bwa.unique.bam SAMstats-DS70_Mu3-CRR995032.2x36mers.noMT.bwa.unique -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py DS70_Pl1-CRR995033.2x36mers.noMT.bwa.unique.bam SAMstats-DS70_Pl1-CRR995033.2x36mers.noMT.bwa.unique -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py DS70_Pl3-CRR995034.2x36mers.noMT.bwa.unique.bam SAMstats-DS70_Pl3-CRR995034.2x36mers.noMT.bwa.unique -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py LB115_Br1-CRR995035.2x36mers.noMT.bwa.unique.bam SAMstats-LB115_Br1-CRR995035.2x36mers.noMT.bwa.unique -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py LB115_Br2-CRR995036.2x36mers.noMT.bwa.unique.bam SAMstats-LB115_Br2-CRR995036.2x36mers.noMT.bwa.unique -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py LB115_Br3-CRR995037.2x36mers.noMT.bwa.unique.bam SAMstats-LB115_Br3-CRR995037.2x36mers.noMT.bwa.unique -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py LB115_Li1-CRR995038.2x36mers.noMT.bwa.unique.bam SAMstats-LB115_Li1-CRR995038.2x36mers.noMT.bwa.unique -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py LB115_Li2-CRR995039.2x36mers.noMT.bwa.unique.bam SAMstats-LB115_Li2-CRR995039.2x36mers.noMT.bwa.unique -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py LB115_Li3-CRR995040.2x36mers.noMT.bwa.unique.bam SAMstats-LB115_Li3-CRR995040.2x36mers.noMT.bwa.unique -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py LB115_Mu1-CRR995041.2x36mers.noMT.bwa.unique.bam SAMstats-LB115_Mu1-CRR995041.2x36mers.noMT.bwa.unique -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py LB115_Mu2-CRR995042.2x36mers.noMT.bwa.unique.bam SAMstats-LB115_Mu2-CRR995042.2x36mers.noMT.bwa.unique -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py LB115_Mu3-CRR995043.2x36mers.noMT.bwa.unique.bam SAMstats-LB115_Mu3-CRR995043.2x36mers.noMT.bwa.unique -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py LB168_F_Br2-CRR995044.2x36mers.noMT.bwa.unique.bam SAMstats-LB168_F_Br2-CRR995044.2x36mers.noMT.bwa.unique -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py LB168_F_Li2-CRR995045.2x36mers.noMT.bwa.unique.bam SAMstats-LB168_F_Li2-CRR995045.2x36mers.noMT.bwa.unique -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py LB168_F_Mu2-CRR995046.2x36mers.noMT.bwa.unique.bam SAMstats-LB168_F_Mu2-CRR995046.2x36mers.noMT.bwa.unique -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py LB168_G_Br1-CRR995047.2x36mers.noMT.bwa.unique.bam SAMstats-LB168_G_Br1-CRR995047.2x36mers.noMT.bwa.unique -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py LB168_G_Li1-CRR995048.2x36mers.noMT.bwa.unique.bam SAMstats-LB168_G_Li1-CRR995048.2x36mers.noMT.bwa.unique -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py LB168_G_Mu1-CRR995049.2x36mers.noMT.bwa.unique.bam SAMstats-LB168_G_Mu1-CRR995049.2x36mers.noMT.bwa.unique -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py LB168_H_Br3-CRR995050.2x36mers.noMT.bwa.unique.bam SAMstats-LB168_H_Br3-CRR995050.2x36mers.noMT.bwa.unique -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py LB168_H_Li3-CRR995051.2x36mers.noMT.bwa.unique.bam SAMstats-LB168_H_Li3-CRR995051.2x36mers.noMT.bwa.unique -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py LB168_H_Mu3-CRR995052.2x36mers.noMT.bwa.unique.bam SAMstats-LB168_H_Mu3-CRR995052.2x36mers.noMT.bwa.unique -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py LB40_Br1-CRR995053.2x36mers.noMT.bwa.unique.bam SAMstats-LB40_Br1-CRR995053.2x36mers.noMT.bwa.unique -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py LB40_Br3-CRR995055.2x36mers.noMT.bwa.unique.bam SAMstats-LB40_Br3-CRR995055.2x36mers.noMT.bwa.unique -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py LB40_Li1-CRR995056.2x36mers.noMT.bwa.unique.bam SAMstats-LB40_Li1-CRR995056.2x36mers.noMT.bwa.unique -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py LB40_Li2-CRR995057.2x36mers.noMT.bwa.unique.bam SAMstats-LB40_Li2-CRR995057.2x36mers.noMT.bwa.unique -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py LB40_Li3-CRR995058.2x36mers.noMT.bwa.unique.bam SAMstats-LB40_Li3-CRR995058.2x36mers.noMT.bwa.unique -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py LB40_Mu2-CRR995060.2x36mers.noMT.bwa.unique.bam SAMstats-LB40_Mu2-CRR995060.2x36mers.noMT.bwa.unique -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py LB40_Mu3-CRR995061.2x36mers.noMT.bwa.unique.bam SAMstats-LB40_Mu3-CRR995061.2x36mers.noMT.bwa.unique -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py LB40_Pl1-CRR995062.2x36mers.noMT.bwa.unique.bam SAMstats-LB40_Pl1-CRR995062.2x36mers.noMT.bwa.unique -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py LB40_Pl2-CRR995063.2x36mers.noMT.bwa.unique.bam SAMstats-LB40_Pl2-CRR995063.2x36mers.noMT.bwa.unique -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py LB40_Pl3-CRR995064.2x36mers.noMT.bwa.unique.bam SAMstats-LB40_Pl3-CRR995064.2x36mers.noMT.bwa.unique -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py LB70_Br1-CRR995065.2x36mers.noMT.bwa.unique.bam SAMstats-LB70_Br1-CRR995065.2x36mers.noMT.bwa.unique -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py LB70_Br2-CRR995066.2x36mers.noMT.bwa.unique.bam SAMstats-LB70_Br2-CRR995066.2x36mers.noMT.bwa.unique -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py LB70_Br3-CRR995067.2x36mers.noMT.bwa.unique.bam SAMstats-LB70_Br3-CRR995067.2x36mers.noMT.bwa.unique -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py LB70_Li1-CRR995068.2x36mers.noMT.bwa.unique.bam SAMstats-LB70_Li1-CRR995068.2x36mers.noMT.bwa.unique -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py LB70_Li2-CRR995069.2x36mers.noMT.bwa.unique.bam SAMstats-LB70_Li2-CRR995069.2x36mers.noMT.bwa.unique -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py LB70_Li3-CRR995070.2x36mers.noMT.bwa.unique.bam SAMstats-LB70_Li3-CRR995070.2x36mers.noMT.bwa.unique -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py LB70_Mu1-CRR995071.2x36mers.noMT.bwa.unique.bam SAMstats-LB70_Mu1-CRR995071.2x36mers.noMT.bwa.unique -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py LB70_Mu2-CRR995072.2x36mers.noMT.bwa.unique.bam SAMstats-LB70_Mu2-CRR995072.2x36mers.noMT.bwa.unique -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py LB70_Mu3-CRR995073.2x36mers.noMT.bwa.unique.bam SAMstats-LB70_Mu3-CRR995073.2x36mers.noMT.bwa.unique -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py LB70_Pl1-CRR995074.2x36mers.noMT.bwa.unique.bam SAMstats-LB70_Pl1-CRR995074.2x36mers.noMT.bwa.unique -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py LB70_Pl2-CRR995075.2x36mers.noMT.bwa.unique.bam SAMstats-LB70_Pl2-CRR995075.2x36mers.noMT.bwa.unique -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py LB70_Pl3-CRR995076.2x36mers.noMT.bwa.unique.bam SAMstats-LB70_Pl3-CRR995076.2x36mers.noMT.bwa.unique -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py LS115_Br1-CRR995077.2x36mers.noMT.bwa.unique.bam SAMstats-LS115_Br1-CRR995077.2x36mers.noMT.bwa.unique -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py LS115_Br2-CRR995078.2x36mers.noMT.bwa.unique.bam SAMstats-LS115_Br2-CRR995078.2x36mers.noMT.bwa.unique -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py LS115_Br3-CRR995079.2x36mers.noMT.bwa.unique.bam SAMstats-LS115_Br3-CRR995079.2x36mers.noMT.bwa.unique -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py LS115_Li1-CRR995080.2x36mers.noMT.bwa.unique.bam SAMstats-LS115_Li1-CRR995080.2x36mers.noMT.bwa.unique -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py LS115_Li2-CRR995081.2x36mers.noMT.bwa.unique.bam SAMstats-LS115_Li2-CRR995081.2x36mers.noMT.bwa.unique -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py LS115_Li3-CRR995082.2x36mers.noMT.bwa.unique.bam SAMstats-LS115_Li3-CRR995082.2x36mers.noMT.bwa.unique -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py LS115_Mu1-CRR995083.2x36mers.noMT.bwa.unique.bam SAMstats-LS115_Mu1-CRR995083.2x36mers.noMT.bwa.unique -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py LS115_Mu2-CRR995084.2x36mers.noMT.bwa.unique.bam SAMstats-LS115_Mu2-CRR995084.2x36mers.noMT.bwa.unique -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py LS115_Mu3-CRR995085.2x36mers.noMT.bwa.unique.bam SAMstats-LS115_Mu3-CRR995085.2x36mers.noMT.bwa.unique -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py LS168_B_Li1-CRR995087.2x36mers.noMT.bwa.unique.bam SAMstats-LS168_B_Li1-CRR995087.2x36mers.noMT.bwa.unique -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py LS168_B_Mu1-CRR995088.2x36mers.noMT.bwa.unique.bam SAMstats-LS168_B_Mu1-CRR995088.2x36mers.noMT.bwa.unique -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py LS168_C_Br2-CRR995089.2x36mers.noMT.bwa.unique.bam SAMstats-LS168_C_Br2-CRR995089.2x36mers.noMT.bwa.unique -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py LS168_C_Li2-CRR995090.2x36mers.noMT.bwa.unique.bam SAMstats-LS168_C_Li2-CRR995090.2x36mers.noMT.bwa.unique -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py LS168_C_Mu2-CRR995091.2x36mers.noMT.bwa.unique.bam SAMstats-LS168_C_Mu2-CRR995091.2x36mers.noMT.bwa.unique -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py LS168_L_Li3-CRR995092.2x36mers.noMT.bwa.unique.bam SAMstats-LS168_L_Li3-CRR995092.2x36mers.noMT.bwa.unique -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py LS40_Br2-CRR995095.2x36mers.noMT.bwa.unique.bam SAMstats-LS40_Br2-CRR995095.2x36mers.noMT.bwa.unique -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py LS40_Br3-CRR995096.2x36mers.noMT.bwa.unique.bam SAMstats-LS40_Br3-CRR995096.2x36mers.noMT.bwa.unique -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py LS40_Li1-CRR995097.2x36mers.noMT.bwa.unique.bam SAMstats-LS40_Li1-CRR995097.2x36mers.noMT.bwa.unique -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py LS40_Li2-CRR995098.2x36mers.noMT.bwa.unique.bam SAMstats-LS40_Li2-CRR995098.2x36mers.noMT.bwa.unique -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py LS40_Li3-CRR995099.2x36mers.noMT.bwa.unique.bam SAMstats-LS40_Li3-CRR995099.2x36mers.noMT.bwa.unique -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py LS40_Mu1-CRR995100.2x36mers.noMT.bwa.unique.bam SAMstats-LS40_Mu1-CRR995100.2x36mers.noMT.bwa.unique -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py LS40_Mu2-CRR995101.2x36mers.noMT.bwa.unique.bam SAMstats-LS40_Mu2-CRR995101.2x36mers.noMT.bwa.unique -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py LS40_Mu3-CRR995102.2x36mers.noMT.bwa.unique.bam SAMstats-LS40_Mu3-CRR995102.2x36mers.noMT.bwa.unique -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py LS40_Pl1-CRR995103.2x36mers.noMT.bwa.unique.bam SAMstats-LS40_Pl1-CRR995103.2x36mers.noMT.bwa.unique -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py LS40_Pl2-CRR995104.2x36mers.noMT.bwa.unique.bam SAMstats-LS40_Pl2-CRR995104.2x36mers.noMT.bwa.unique -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py LS40_Pl3-CRR995105.2x36mers.noMT.bwa.unique.bam SAMstats-LS40_Pl3-CRR995105.2x36mers.noMT.bwa.unique -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py LS70_Br1-CRR995106.2x36mers.noMT.bwa.unique.bam SAMstats-LS70_Br1-CRR995106.2x36mers.noMT.bwa.unique -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py LS70_Br2-CRR995107.2x36mers.noMT.bwa.unique.bam SAMstats-LS70_Br2-CRR995107.2x36mers.noMT.bwa.unique -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py LS70_Br3-CRR995108.2x36mers.noMT.bwa.unique.bam SAMstats-LS70_Br3-CRR995108.2x36mers.noMT.bwa.unique -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py LS70_Li1-CRR995109.2x36mers.noMT.bwa.unique.bam SAMstats-LS70_Li1-CRR995109.2x36mers.noMT.bwa.unique -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py LS70_Li2-CRR995110.2x36mers.noMT.bwa.unique.bam SAMstats-LS70_Li2-CRR995110.2x36mers.noMT.bwa.unique -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py LS70_Li3-CRR995111.2x36mers.noMT.bwa.unique.bam SAMstats-LS70_Li3-CRR995111.2x36mers.noMT.bwa.unique -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py LS70_Mu1-CRR995112.2x36mers.noMT.bwa.unique.bam SAMstats-LS70_Mu1-CRR995112.2x36mers.noMT.bwa.unique -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py LS70_Mu2-CRR995113.2x36mers.noMT.bwa.unique.bam SAMstats-LS70_Mu2-CRR995113.2x36mers.noMT.bwa.unique -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py LS70_Mu3-CRR995114.2x36mers.noMT.bwa.unique.bam SAMstats-LS70_Mu3-CRR995114.2x36mers.noMT.bwa.unique -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py LS70_Pl2-CRR995115.2x36mers.noMT.bwa.unique.bam SAMstats-LS70_Pl2-CRR995115.2x36mers.noMT.bwa.unique -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py LS70_Pl3-CRR995116.2x36mers.noMT.bwa.unique.bam SAMstats-LS70_Pl3-CRR995116.2x36mers.noMT.bwa.unique -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py DB115_Br2-CRR994956.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes DB115_Br2-CRR994956.2x36mers.noMT.bwa.unique.dedup.InsLen -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py DB115_Br3-CRR994957.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes DB115_Br3-CRR994957.2x36mers.noMT.bwa.unique.dedup.InsLen -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py DB115_Li2-CRR994959.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes DB115_Li2-CRR994959.2x36mers.noMT.bwa.unique.dedup.InsLen -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py DB115_Li3-CRR994960.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes DB115_Li3-CRR994960.2x36mers.noMT.bwa.unique.dedup.InsLen -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py DB115_Mu1-CRR994961.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes DB115_Mu1-CRR994961.2x36mers.noMT.bwa.unique.dedup.InsLen -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py DB115_Mu2-CRR994962.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes DB115_Mu2-CRR994962.2x36mers.noMT.bwa.unique.dedup.InsLen -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py DB115_Mu3-CRR994963.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes DB115_Mu3-CRR994963.2x36mers.noMT.bwa.unique.dedup.InsLen -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py DB168_E_Br1-CRR994964.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes DB168_E_Br1-CRR994964.2x36mers.noMT.bwa.unique.dedup.InsLen -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py DB168_E_Li1-CRR994965.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes DB168_E_Li1-CRR994965.2x36mers.noMT.bwa.unique.dedup.InsLen -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py DB168_I_Br2-CRR994967.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes DB168_I_Br2-CRR994967.2x36mers.noMT.bwa.unique.dedup.InsLen -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py DB168_I_Li2-CRR994968.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes DB168_I_Li2-CRR994968.2x36mers.noMT.bwa.unique.dedup.InsLen -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py DB168_I_Mu2-CRR994969.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes DB168_I_Mu2-CRR994969.2x36mers.noMT.bwa.unique.dedup.InsLen -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py DB168_J_Br3-CRR994970.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes DB168_J_Br3-CRR994970.2x36mers.noMT.bwa.unique.dedup.InsLen -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py DB168_J_Li3-CRR994971.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes DB168_J_Li3-CRR994971.2x36mers.noMT.bwa.unique.dedup.InsLen -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py DB168_J_Mu3-CRR994972.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes DB168_J_Mu3-CRR994972.2x36mers.noMT.bwa.unique.dedup.InsLen -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py DB40_Br1-CRR994973.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes DB40_Br1-CRR994973.2x36mers.noMT.bwa.unique.dedup.InsLen -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py DB40_Li1-CRR994976.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes DB40_Li1-CRR994976.2x36mers.noMT.bwa.unique.dedup.InsLen -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py DB40_Li2-CRR994977.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes DB40_Li2-CRR994977.2x36mers.noMT.bwa.unique.dedup.InsLen -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py DB40_Li3-CRR994978.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes DB40_Li3-CRR994978.2x36mers.noMT.bwa.unique.dedup.InsLen -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py DB40_Mu1-CRR994979.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes DB40_Mu1-CRR994979.2x36mers.noMT.bwa.unique.dedup.InsLen -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py DB40_Mu2-CRR994980.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes DB40_Mu2-CRR994980.2x36mers.noMT.bwa.unique.dedup.InsLen -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py DB40_Mu3-CRR994981.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes DB40_Mu3-CRR994981.2x36mers.noMT.bwa.unique.dedup.InsLen -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py DB40_Pl1-CRR994982.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes DB40_Pl1-CRR994982.2x36mers.noMT.bwa.unique.dedup.InsLen -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py DB40_Pl2-CRR994983.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes DB40_Pl2-CRR994983.2x36mers.noMT.bwa.unique.dedup.InsLen -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py DB40_Pl3-CRR994984.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes DB40_Pl3-CRR994984.2x36mers.noMT.bwa.unique.dedup.InsLen -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py DB70_Br1-CRR994985.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes DB70_Br1-CRR994985.2x36mers.noMT.bwa.unique.dedup.InsLen -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py DB70_Br3-CRR994987.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes DB70_Br3-CRR994987.2x36mers.noMT.bwa.unique.dedup.InsLen -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py DB70_Li2-CRR994989.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes DB70_Li2-CRR994989.2x36mers.noMT.bwa.unique.dedup.InsLen -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py DB70_Li3-CRR994990.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes DB70_Li3-CRR994990.2x36mers.noMT.bwa.unique.dedup.InsLen -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py DB70_Mu1-CRR994991.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes DB70_Mu1-CRR994991.2x36mers.noMT.bwa.unique.dedup.InsLen -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py DB70_Mu2-CRR994992.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes DB70_Mu2-CRR994992.2x36mers.noMT.bwa.unique.dedup.InsLen -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py DB70_Mu3-CRR994993.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes DB70_Mu3-CRR994993.2x36mers.noMT.bwa.unique.dedup.InsLen -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py DB70_Pl1-CRR994994.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes DB70_Pl1-CRR994994.2x36mers.noMT.bwa.unique.dedup.InsLen -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py DS115_Br1-CRR994995.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes DS115_Br1-CRR994995.2x36mers.noMT.bwa.unique.dedup.InsLen -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py DS115_Br2-CRR994996.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes DS115_Br2-CRR994996.2x36mers.noMT.bwa.unique.dedup.InsLen -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py DS115_Br3-CRR994997.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes DS115_Br3-CRR994997.2x36mers.noMT.bwa.unique.dedup.InsLen -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py DS115_Li1-CRR994998.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes DS115_Li1-CRR994998.2x36mers.noMT.bwa.unique.dedup.InsLen -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py DS115_Li2-CRR994999.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes DS115_Li2-CRR994999.2x36mers.noMT.bwa.unique.dedup.InsLen -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py DS115_Li3-CRR995000.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes DS115_Li3-CRR995000.2x36mers.noMT.bwa.unique.dedup.InsLen -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py DS115_Mu1-CRR995001.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes DS115_Mu1-CRR995001.2x36mers.noMT.bwa.unique.dedup.InsLen -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py DS115_Mu2-CRR995002.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes DS115_Mu2-CRR995002.2x36mers.noMT.bwa.unique.dedup.InsLen -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py DS115_Mu3-CRR995003.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes DS115_Mu3-CRR995003.2x36mers.noMT.bwa.unique.dedup.InsLen -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py DS168_M_Br1-CRR995004.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes DS168_M_Br1-CRR995004.2x36mers.noMT.bwa.unique.dedup.InsLen -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py DS168_M_Li1-CRR995005.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes DS168_M_Li1-CRR995005.2x36mers.noMT.bwa.unique.dedup.InsLen -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py DS168_N_Br2-CRR995007.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes DS168_N_Br2-CRR995007.2x36mers.noMT.bwa.unique.dedup.InsLen -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py DS168_N_Li2-CRR995008.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes DS168_N_Li2-CRR995008.2x36mers.noMT.bwa.unique.dedup.InsLen -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py DS168_N_Mu2-CRR995009.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes DS168_N_Mu2-CRR995009.2x36mers.noMT.bwa.unique.dedup.InsLen -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py DS168_O_Br3-CRR995010.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes DS168_O_Br3-CRR995010.2x36mers.noMT.bwa.unique.dedup.InsLen -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py DS168_O_Li3-CRR995011.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes DS168_O_Li3-CRR995011.2x36mers.noMT.bwa.unique.dedup.InsLen -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py DS40_Br1-CRR995013.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes DS40_Br1-CRR995013.2x36mers.noMT.bwa.unique.dedup.InsLen -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py DS40_Br2-CRR995014.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes DS40_Br2-CRR995014.2x36mers.noMT.bwa.unique.dedup.InsLen -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py DS40_Br3-CRR995015.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes DS40_Br3-CRR995015.2x36mers.noMT.bwa.unique.dedup.InsLen -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py DS40_Li2-CRR995016.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes DS40_Li2-CRR995016.2x36mers.noMT.bwa.unique.dedup.InsLen -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py DS40_Li3-CRR995017.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes DS40_Li3-CRR995017.2x36mers.noMT.bwa.unique.dedup.InsLen -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py DS40_Mu1-CRR995018.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes DS40_Mu1-CRR995018.2x36mers.noMT.bwa.unique.dedup.InsLen -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py DS40_Mu2-CRR995019.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes DS40_Mu2-CRR995019.2x36mers.noMT.bwa.unique.dedup.InsLen -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py DS40_Mu3-CRR995020.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes DS40_Mu3-CRR995020.2x36mers.noMT.bwa.unique.dedup.InsLen -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py DS40_Pl1-CRR995021.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes DS40_Pl1-CRR995021.2x36mers.noMT.bwa.unique.dedup.InsLen -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py DS40_Pl2-CRR995022.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes DS40_Pl2-CRR995022.2x36mers.noMT.bwa.unique.dedup.InsLen -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py DS40_Pl3-CRR995023.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes DS40_Pl3-CRR995023.2x36mers.noMT.bwa.unique.dedup.InsLen -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py DS70_Br1-CRR995024.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes DS70_Br1-CRR995024.2x36mers.noMT.bwa.unique.dedup.InsLen -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py DS70_Br2-CRR995025.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes DS70_Br2-CRR995025.2x36mers.noMT.bwa.unique.dedup.InsLen -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py DS70_Br3-CRR995026.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes DS70_Br3-CRR995026.2x36mers.noMT.bwa.unique.dedup.InsLen -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py DS70_Li1-CRR995027.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes DS70_Li1-CRR995027.2x36mers.noMT.bwa.unique.dedup.InsLen -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py DS70_Li2-CRR995028.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes DS70_Li2-CRR995028.2x36mers.noMT.bwa.unique.dedup.InsLen -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py DS70_Li3-CRR995029.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes DS70_Li3-CRR995029.2x36mers.noMT.bwa.unique.dedup.InsLen -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py DS70_Mu1-CRR995030.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes DS70_Mu1-CRR995030.2x36mers.noMT.bwa.unique.dedup.InsLen -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py DS70_Mu2-CRR995031.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes DS70_Mu2-CRR995031.2x36mers.noMT.bwa.unique.dedup.InsLen -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py DS70_Mu3-CRR995032.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes DS70_Mu3-CRR995032.2x36mers.noMT.bwa.unique.dedup.InsLen -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py DS70_Pl1-CRR995033.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes DS70_Pl1-CRR995033.2x36mers.noMT.bwa.unique.dedup.InsLen -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py DS70_Pl3-CRR995034.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes DS70_Pl3-CRR995034.2x36mers.noMT.bwa.unique.dedup.InsLen -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py LB115_Br1-CRR995035.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes LB115_Br1-CRR995035.2x36mers.noMT.bwa.unique.dedup.InsLen -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py LB115_Br2-CRR995036.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes LB115_Br2-CRR995036.2x36mers.noMT.bwa.unique.dedup.InsLen -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py LB115_Br3-CRR995037.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes LB115_Br3-CRR995037.2x36mers.noMT.bwa.unique.dedup.InsLen -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py LB115_Li1-CRR995038.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes LB115_Li1-CRR995038.2x36mers.noMT.bwa.unique.dedup.InsLen -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py LB115_Li2-CRR995039.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes LB115_Li2-CRR995039.2x36mers.noMT.bwa.unique.dedup.InsLen -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py LB115_Li3-CRR995040.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes LB115_Li3-CRR995040.2x36mers.noMT.bwa.unique.dedup.InsLen -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py LB115_Mu1-CRR995041.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes LB115_Mu1-CRR995041.2x36mers.noMT.bwa.unique.dedup.InsLen -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py LB115_Mu2-CRR995042.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes LB115_Mu2-CRR995042.2x36mers.noMT.bwa.unique.dedup.InsLen -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py LB115_Mu3-CRR995043.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes LB115_Mu3-CRR995043.2x36mers.noMT.bwa.unique.dedup.InsLen -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py LB168_F_Br2-CRR995044.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes LB168_F_Br2-CRR995044.2x36mers.noMT.bwa.unique.dedup.InsLen -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py LB168_F_Li2-CRR995045.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes LB168_F_Li2-CRR995045.2x36mers.noMT.bwa.unique.dedup.InsLen -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py LB168_F_Mu2-CRR995046.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes LB168_F_Mu2-CRR995046.2x36mers.noMT.bwa.unique.dedup.InsLen -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py LB168_G_Br1-CRR995047.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes LB168_G_Br1-CRR995047.2x36mers.noMT.bwa.unique.dedup.InsLen -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py LB168_G_Li1-CRR995048.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes LB168_G_Li1-CRR995048.2x36mers.noMT.bwa.unique.dedup.InsLen -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py LB168_G_Mu1-CRR995049.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes LB168_G_Mu1-CRR995049.2x36mers.noMT.bwa.unique.dedup.InsLen -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py LB168_H_Br3-CRR995050.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes LB168_H_Br3-CRR995050.2x36mers.noMT.bwa.unique.dedup.InsLen -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py LB168_H_Li3-CRR995051.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes LB168_H_Li3-CRR995051.2x36mers.noMT.bwa.unique.dedup.InsLen -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py LB168_H_Mu3-CRR995052.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes LB168_H_Mu3-CRR995052.2x36mers.noMT.bwa.unique.dedup.InsLen -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py LB40_Br1-CRR995053.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes LB40_Br1-CRR995053.2x36mers.noMT.bwa.unique.dedup.InsLen -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py LB40_Br3-CRR995055.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes LB40_Br3-CRR995055.2x36mers.noMT.bwa.unique.dedup.InsLen -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py LB40_Li1-CRR995056.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes LB40_Li1-CRR995056.2x36mers.noMT.bwa.unique.dedup.InsLen -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py LB40_Li2-CRR995057.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes LB40_Li2-CRR995057.2x36mers.noMT.bwa.unique.dedup.InsLen -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py LB40_Li3-CRR995058.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes LB40_Li3-CRR995058.2x36mers.noMT.bwa.unique.dedup.InsLen -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py LB40_Mu2-CRR995060.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes LB40_Mu2-CRR995060.2x36mers.noMT.bwa.unique.dedup.InsLen -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py LB40_Mu3-CRR995061.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes LB40_Mu3-CRR995061.2x36mers.noMT.bwa.unique.dedup.InsLen -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py LB40_Pl1-CRR995062.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes LB40_Pl1-CRR995062.2x36mers.noMT.bwa.unique.dedup.InsLen -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py LB40_Pl2-CRR995063.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes LB40_Pl2-CRR995063.2x36mers.noMT.bwa.unique.dedup.InsLen -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py LB40_Pl3-CRR995064.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes LB40_Pl3-CRR995064.2x36mers.noMT.bwa.unique.dedup.InsLen -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py LB70_Br1-CRR995065.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes LB70_Br1-CRR995065.2x36mers.noMT.bwa.unique.dedup.InsLen -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py LB70_Br2-CRR995066.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes LB70_Br2-CRR995066.2x36mers.noMT.bwa.unique.dedup.InsLen -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py LB70_Br3-CRR995067.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes LB70_Br3-CRR995067.2x36mers.noMT.bwa.unique.dedup.InsLen -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py LB70_Li1-CRR995068.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes LB70_Li1-CRR995068.2x36mers.noMT.bwa.unique.dedup.InsLen -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py LB70_Li2-CRR995069.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes LB70_Li2-CRR995069.2x36mers.noMT.bwa.unique.dedup.InsLen -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py LB70_Li3-CRR995070.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes LB70_Li3-CRR995070.2x36mers.noMT.bwa.unique.dedup.InsLen -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py LB70_Mu1-CRR995071.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes LB70_Mu1-CRR995071.2x36mers.noMT.bwa.unique.dedup.InsLen -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py LB70_Mu2-CRR995072.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes LB70_Mu2-CRR995072.2x36mers.noMT.bwa.unique.dedup.InsLen -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py LB70_Mu3-CRR995073.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes LB70_Mu3-CRR995073.2x36mers.noMT.bwa.unique.dedup.InsLen -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py LB70_Pl1-CRR995074.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes LB70_Pl1-CRR995074.2x36mers.noMT.bwa.unique.dedup.InsLen -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py LB70_Pl2-CRR995075.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes LB70_Pl2-CRR995075.2x36mers.noMT.bwa.unique.dedup.InsLen -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py LB70_Pl3-CRR995076.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes LB70_Pl3-CRR995076.2x36mers.noMT.bwa.unique.dedup.InsLen -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py LS115_Br1-CRR995077.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes LS115_Br1-CRR995077.2x36mers.noMT.bwa.unique.dedup.InsLen -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py LS115_Br2-CRR995078.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes LS115_Br2-CRR995078.2x36mers.noMT.bwa.unique.dedup.InsLen -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py LS115_Br3-CRR995079.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes LS115_Br3-CRR995079.2x36mers.noMT.bwa.unique.dedup.InsLen -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py LS115_Li1-CRR995080.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes LS115_Li1-CRR995080.2x36mers.noMT.bwa.unique.dedup.InsLen -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py LS115_Li2-CRR995081.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes LS115_Li2-CRR995081.2x36mers.noMT.bwa.unique.dedup.InsLen -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py LS115_Li3-CRR995082.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes LS115_Li3-CRR995082.2x36mers.noMT.bwa.unique.dedup.InsLen -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py LS115_Mu1-CRR995083.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes LS115_Mu1-CRR995083.2x36mers.noMT.bwa.unique.dedup.InsLen -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py LS115_Mu2-CRR995084.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes LS115_Mu2-CRR995084.2x36mers.noMT.bwa.unique.dedup.InsLen -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py LS115_Mu3-CRR995085.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes LS115_Mu3-CRR995085.2x36mers.noMT.bwa.unique.dedup.InsLen -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py LS168_B_Li1-CRR995087.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes LS168_B_Li1-CRR995087.2x36mers.noMT.bwa.unique.dedup.InsLen -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py LS168_B_Mu1-CRR995088.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes LS168_B_Mu1-CRR995088.2x36mers.noMT.bwa.unique.dedup.InsLen -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py LS168_C_Br2-CRR995089.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes LS168_C_Br2-CRR995089.2x36mers.noMT.bwa.unique.dedup.InsLen -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py LS168_C_Li2-CRR995090.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes LS168_C_Li2-CRR995090.2x36mers.noMT.bwa.unique.dedup.InsLen -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py LS168_C_Mu2-CRR995091.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes LS168_C_Mu2-CRR995091.2x36mers.noMT.bwa.unique.dedup.InsLen -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py LS168_L_Li3-CRR995092.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes LS168_L_Li3-CRR995092.2x36mers.noMT.bwa.unique.dedup.InsLen -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py LS40_Br2-CRR995095.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes LS40_Br2-CRR995095.2x36mers.noMT.bwa.unique.dedup.InsLen -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py LS40_Br3-CRR995096.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes LS40_Br3-CRR995096.2x36mers.noMT.bwa.unique.dedup.InsLen -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py LS40_Li1-CRR995097.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes LS40_Li1-CRR995097.2x36mers.noMT.bwa.unique.dedup.InsLen -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py LS40_Li2-CRR995098.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes LS40_Li2-CRR995098.2x36mers.noMT.bwa.unique.dedup.InsLen -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py LS40_Li3-CRR995099.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes LS40_Li3-CRR995099.2x36mers.noMT.bwa.unique.dedup.InsLen -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py LS40_Mu1-CRR995100.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes LS40_Mu1-CRR995100.2x36mers.noMT.bwa.unique.dedup.InsLen -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py LS40_Mu2-CRR995101.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes LS40_Mu2-CRR995101.2x36mers.noMT.bwa.unique.dedup.InsLen -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py LS40_Mu3-CRR995102.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes LS40_Mu3-CRR995102.2x36mers.noMT.bwa.unique.dedup.InsLen -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py LS40_Pl1-CRR995103.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes LS40_Pl1-CRR995103.2x36mers.noMT.bwa.unique.dedup.InsLen -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py LS40_Pl2-CRR995104.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes LS40_Pl2-CRR995104.2x36mers.noMT.bwa.unique.dedup.InsLen -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py LS40_Pl3-CRR995105.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes LS40_Pl3-CRR995105.2x36mers.noMT.bwa.unique.dedup.InsLen -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py LS70_Br1-CRR995106.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes LS70_Br1-CRR995106.2x36mers.noMT.bwa.unique.dedup.InsLen -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py LS70_Br2-CRR995107.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes LS70_Br2-CRR995107.2x36mers.noMT.bwa.unique.dedup.InsLen -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py LS70_Br3-CRR995108.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes LS70_Br3-CRR995108.2x36mers.noMT.bwa.unique.dedup.InsLen -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py LS70_Li1-CRR995109.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes LS70_Li1-CRR995109.2x36mers.noMT.bwa.unique.dedup.InsLen -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py LS70_Li2-CRR995110.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes LS70_Li2-CRR995110.2x36mers.noMT.bwa.unique.dedup.InsLen -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py LS70_Li3-CRR995111.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes LS70_Li3-CRR995111.2x36mers.noMT.bwa.unique.dedup.InsLen -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py LS70_Mu1-CRR995112.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes LS70_Mu1-CRR995112.2x36mers.noMT.bwa.unique.dedup.InsLen -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py LS70_Mu2-CRR995113.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes LS70_Mu2-CRR995113.2x36mers.noMT.bwa.unique.dedup.InsLen -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py LS70_Mu3-CRR995114.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes LS70_Mu3-CRR995114.2x36mers.noMT.bwa.unique.dedup.InsLen -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py LS70_Pl2-CRR995115.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes LS70_Pl2-CRR995115.2x36mers.noMT.bwa.unique.dedup.InsLen -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py LS70_Pl3-CRR995116.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes LS70_Pl3-CRR995116.2x36mers.noMT.bwa.unique.dedup.InsLen -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- DB115_Br2-CRR994956.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes DB115_Br2-CRR994956.2x36mers.noMT.bwa.unique.dedup.wig -notitle -uniqueBAM -RPM &
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- DB115_Br3-CRR994957.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes DB115_Br3-CRR994957.2x36mers.noMT.bwa.unique.dedup.wig -notitle -uniqueBAM -RPM &
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- DB115_Li2-CRR994959.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes DB115_Li2-CRR994959.2x36mers.noMT.bwa.unique.dedup.wig -notitle -uniqueBAM -RPM &
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- DB115_Li3-CRR994960.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes DB115_Li3-CRR994960.2x36mers.noMT.bwa.unique.dedup.wig -notitle -uniqueBAM -RPM &
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- DB115_Mu1-CRR994961.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes DB115_Mu1-CRR994961.2x36mers.noMT.bwa.unique.dedup.wig -notitle -uniqueBAM -RPM &
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- DB115_Mu2-CRR994962.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes DB115_Mu2-CRR994962.2x36mers.noMT.bwa.unique.dedup.wig -notitle -uniqueBAM -RPM &
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- DB115_Mu3-CRR994963.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes DB115_Mu3-CRR994963.2x36mers.noMT.bwa.unique.dedup.wig -notitle -uniqueBAM -RPM &
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- DB168_E_Br1-CRR994964.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes DB168_E_Br1-CRR994964.2x36mers.noMT.bwa.unique.dedup.wig -notitle -uniqueBAM -RPM &
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- DB168_E_Li1-CRR994965.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes DB168_E_Li1-CRR994965.2x36mers.noMT.bwa.unique.dedup.wig -notitle -uniqueBAM -RPM &
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- DB168_I_Br2-CRR994967.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes DB168_I_Br2-CRR994967.2x36mers.noMT.bwa.unique.dedup.wig -notitle -uniqueBAM -RPM &
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- DB168_I_Li2-CRR994968.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes DB168_I_Li2-CRR994968.2x36mers.noMT.bwa.unique.dedup.wig -notitle -uniqueBAM -RPM &
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- DB168_I_Mu2-CRR994969.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes DB168_I_Mu2-CRR994969.2x36mers.noMT.bwa.unique.dedup.wig -notitle -uniqueBAM -RPM &
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- DB168_J_Br3-CRR994970.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes DB168_J_Br3-CRR994970.2x36mers.noMT.bwa.unique.dedup.wig -notitle -uniqueBAM -RPM &
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- DB168_J_Li3-CRR994971.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes DB168_J_Li3-CRR994971.2x36mers.noMT.bwa.unique.dedup.wig -notitle -uniqueBAM -RPM &
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- DB168_J_Mu3-CRR994972.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes DB168_J_Mu3-CRR994972.2x36mers.noMT.bwa.unique.dedup.wig -notitle -uniqueBAM -RPM &
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- DB40_Br1-CRR994973.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes DB40_Br1-CRR994973.2x36mers.noMT.bwa.unique.dedup.wig -notitle -uniqueBAM -RPM &
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- DB40_Li1-CRR994976.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes DB40_Li1-CRR994976.2x36mers.noMT.bwa.unique.dedup.wig -notitle -uniqueBAM -RPM &
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- DB40_Li2-CRR994977.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes DB40_Li2-CRR994977.2x36mers.noMT.bwa.unique.dedup.wig -notitle -uniqueBAM -RPM &
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- DB40_Li3-CRR994978.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes DB40_Li3-CRR994978.2x36mers.noMT.bwa.unique.dedup.wig -notitle -uniqueBAM -RPM &
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- DB40_Mu1-CRR994979.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes DB40_Mu1-CRR994979.2x36mers.noMT.bwa.unique.dedup.wig -notitle -uniqueBAM -RPM &
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- DB40_Mu2-CRR994980.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes DB40_Mu2-CRR994980.2x36mers.noMT.bwa.unique.dedup.wig -notitle -uniqueBAM -RPM &
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- DB40_Mu3-CRR994981.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes DB40_Mu3-CRR994981.2x36mers.noMT.bwa.unique.dedup.wig -notitle -uniqueBAM -RPM &
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- DB40_Pl1-CRR994982.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes DB40_Pl1-CRR994982.2x36mers.noMT.bwa.unique.dedup.wig -notitle -uniqueBAM -RPM &
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- DB40_Pl2-CRR994983.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes DB40_Pl2-CRR994983.2x36mers.noMT.bwa.unique.dedup.wig -notitle -uniqueBAM -RPM &
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- DB40_Pl3-CRR994984.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes DB40_Pl3-CRR994984.2x36mers.noMT.bwa.unique.dedup.wig -notitle -uniqueBAM -RPM &
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- DB70_Br1-CRR994985.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes DB70_Br1-CRR994985.2x36mers.noMT.bwa.unique.dedup.wig -notitle -uniqueBAM -RPM &
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- DB70_Br3-CRR994987.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes DB70_Br3-CRR994987.2x36mers.noMT.bwa.unique.dedup.wig -notitle -uniqueBAM -RPM &
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- DB70_Li2-CRR994989.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes DB70_Li2-CRR994989.2x36mers.noMT.bwa.unique.dedup.wig -notitle -uniqueBAM -RPM &
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- DB70_Li3-CRR994990.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes DB70_Li3-CRR994990.2x36mers.noMT.bwa.unique.dedup.wig -notitle -uniqueBAM -RPM &
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- DB70_Mu1-CRR994991.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes DB70_Mu1-CRR994991.2x36mers.noMT.bwa.unique.dedup.wig -notitle -uniqueBAM -RPM &
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- DB70_Mu2-CRR994992.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes DB70_Mu2-CRR994992.2x36mers.noMT.bwa.unique.dedup.wig -notitle -uniqueBAM -RPM &
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- DB70_Mu3-CRR994993.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes DB70_Mu3-CRR994993.2x36mers.noMT.bwa.unique.dedup.wig -notitle -uniqueBAM -RPM &
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- DB70_Pl1-CRR994994.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes DB70_Pl1-CRR994994.2x36mers.noMT.bwa.unique.dedup.wig -notitle -uniqueBAM -RPM &
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- DS115_Br1-CRR994995.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes DS115_Br1-CRR994995.2x36mers.noMT.bwa.unique.dedup.wig -notitle -uniqueBAM -RPM &
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- DS115_Br2-CRR994996.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes DS115_Br2-CRR994996.2x36mers.noMT.bwa.unique.dedup.wig -notitle -uniqueBAM -RPM &
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- DS115_Br3-CRR994997.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes DS115_Br3-CRR994997.2x36mers.noMT.bwa.unique.dedup.wig -notitle -uniqueBAM -RPM &
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- DS115_Li1-CRR994998.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes DS115_Li1-CRR994998.2x36mers.noMT.bwa.unique.dedup.wig -notitle -uniqueBAM -RPM &
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- DS115_Li2-CRR994999.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes DS115_Li2-CRR994999.2x36mers.noMT.bwa.unique.dedup.wig -notitle -uniqueBAM -RPM &
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- DS115_Li3-CRR995000.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes DS115_Li3-CRR995000.2x36mers.noMT.bwa.unique.dedup.wig -notitle -uniqueBAM -RPM &
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- DS115_Mu1-CRR995001.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes DS115_Mu1-CRR995001.2x36mers.noMT.bwa.unique.dedup.wig -notitle -uniqueBAM -RPM &
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- DS115_Mu2-CRR995002.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes DS115_Mu2-CRR995002.2x36mers.noMT.bwa.unique.dedup.wig -notitle -uniqueBAM -RPM &
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- DS115_Mu3-CRR995003.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes DS115_Mu3-CRR995003.2x36mers.noMT.bwa.unique.dedup.wig -notitle -uniqueBAM -RPM &
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- DS168_M_Br1-CRR995004.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes DS168_M_Br1-CRR995004.2x36mers.noMT.bwa.unique.dedup.wig -notitle -uniqueBAM -RPM &
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- DS168_M_Li1-CRR995005.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes DS168_M_Li1-CRR995005.2x36mers.noMT.bwa.unique.dedup.wig -notitle -uniqueBAM -RPM &
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- DS168_N_Br2-CRR995007.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes DS168_N_Br2-CRR995007.2x36mers.noMT.bwa.unique.dedup.wig -notitle -uniqueBAM -RPM &
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- DS168_N_Li2-CRR995008.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes DS168_N_Li2-CRR995008.2x36mers.noMT.bwa.unique.dedup.wig -notitle -uniqueBAM -RPM &
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- DS168_N_Mu2-CRR995009.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes DS168_N_Mu2-CRR995009.2x36mers.noMT.bwa.unique.dedup.wig -notitle -uniqueBAM -RPM &
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- DS168_O_Br3-CRR995010.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes DS168_O_Br3-CRR995010.2x36mers.noMT.bwa.unique.dedup.wig -notitle -uniqueBAM -RPM &
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- DS168_O_Li3-CRR995011.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes DS168_O_Li3-CRR995011.2x36mers.noMT.bwa.unique.dedup.wig -notitle -uniqueBAM -RPM &
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- DS40_Br1-CRR995013.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes DS40_Br1-CRR995013.2x36mers.noMT.bwa.unique.dedup.wig -notitle -uniqueBAM -RPM &
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- DS40_Br2-CRR995014.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes DS40_Br2-CRR995014.2x36mers.noMT.bwa.unique.dedup.wig -notitle -uniqueBAM -RPM &
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- DS40_Br3-CRR995015.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes DS40_Br3-CRR995015.2x36mers.noMT.bwa.unique.dedup.wig -notitle -uniqueBAM -RPM &
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- DS40_Li2-CRR995016.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes DS40_Li2-CRR995016.2x36mers.noMT.bwa.unique.dedup.wig -notitle -uniqueBAM -RPM &
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- DS40_Li3-CRR995017.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes DS40_Li3-CRR995017.2x36mers.noMT.bwa.unique.dedup.wig -notitle -uniqueBAM -RPM &
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- DS40_Mu1-CRR995018.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes DS40_Mu1-CRR995018.2x36mers.noMT.bwa.unique.dedup.wig -notitle -uniqueBAM -RPM &
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- DS40_Mu2-CRR995019.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes DS40_Mu2-CRR995019.2x36mers.noMT.bwa.unique.dedup.wig -notitle -uniqueBAM -RPM &
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- DS40_Mu3-CRR995020.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes DS40_Mu3-CRR995020.2x36mers.noMT.bwa.unique.dedup.wig -notitle -uniqueBAM -RPM &
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- DS40_Pl1-CRR995021.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes DS40_Pl1-CRR995021.2x36mers.noMT.bwa.unique.dedup.wig -notitle -uniqueBAM -RPM &
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- DS40_Pl2-CRR995022.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes DS40_Pl2-CRR995022.2x36mers.noMT.bwa.unique.dedup.wig -notitle -uniqueBAM -RPM &
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- DS40_Pl3-CRR995023.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes DS40_Pl3-CRR995023.2x36mers.noMT.bwa.unique.dedup.wig -notitle -uniqueBAM -RPM &
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- DS70_Br1-CRR995024.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes DS70_Br1-CRR995024.2x36mers.noMT.bwa.unique.dedup.wig -notitle -uniqueBAM -RPM &
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- DS70_Br2-CRR995025.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes DS70_Br2-CRR995025.2x36mers.noMT.bwa.unique.dedup.wig -notitle -uniqueBAM -RPM &
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- DS70_Br3-CRR995026.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes DS70_Br3-CRR995026.2x36mers.noMT.bwa.unique.dedup.wig -notitle -uniqueBAM -RPM &
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- DS70_Li1-CRR995027.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes DS70_Li1-CRR995027.2x36mers.noMT.bwa.unique.dedup.wig -notitle -uniqueBAM -RPM &
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- DS70_Li2-CRR995028.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes DS70_Li2-CRR995028.2x36mers.noMT.bwa.unique.dedup.wig -notitle -uniqueBAM -RPM &
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- DS70_Li3-CRR995029.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes DS70_Li3-CRR995029.2x36mers.noMT.bwa.unique.dedup.wig -notitle -uniqueBAM -RPM &
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- DS70_Mu1-CRR995030.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes DS70_Mu1-CRR995030.2x36mers.noMT.bwa.unique.dedup.wig -notitle -uniqueBAM -RPM &
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- DS70_Mu2-CRR995031.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes DS70_Mu2-CRR995031.2x36mers.noMT.bwa.unique.dedup.wig -notitle -uniqueBAM -RPM &
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- DS70_Mu3-CRR995032.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes DS70_Mu3-CRR995032.2x36mers.noMT.bwa.unique.dedup.wig -notitle -uniqueBAM -RPM &
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- DS70_Pl1-CRR995033.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes DS70_Pl1-CRR995033.2x36mers.noMT.bwa.unique.dedup.wig -notitle -uniqueBAM -RPM &
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- DS70_Pl3-CRR995034.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes DS70_Pl3-CRR995034.2x36mers.noMT.bwa.unique.dedup.wig -notitle -uniqueBAM -RPM &
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- LB115_Br1-CRR995035.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes LB115_Br1-CRR995035.2x36mers.noMT.bwa.unique.dedup.wig -notitle -uniqueBAM -RPM &
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- LB115_Br2-CRR995036.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes LB115_Br2-CRR995036.2x36mers.noMT.bwa.unique.dedup.wig -notitle -uniqueBAM -RPM &
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- LB115_Br3-CRR995037.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes LB115_Br3-CRR995037.2x36mers.noMT.bwa.unique.dedup.wig -notitle -uniqueBAM -RPM &
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- LB115_Li1-CRR995038.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes LB115_Li1-CRR995038.2x36mers.noMT.bwa.unique.dedup.wig -notitle -uniqueBAM -RPM &
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- LB115_Li2-CRR995039.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes LB115_Li2-CRR995039.2x36mers.noMT.bwa.unique.dedup.wig -notitle -uniqueBAM -RPM &
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- LB115_Li3-CRR995040.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes LB115_Li3-CRR995040.2x36mers.noMT.bwa.unique.dedup.wig -notitle -uniqueBAM -RPM &
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- LB115_Mu1-CRR995041.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes LB115_Mu1-CRR995041.2x36mers.noMT.bwa.unique.dedup.wig -notitle -uniqueBAM -RPM &
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- LB115_Mu2-CRR995042.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes LB115_Mu2-CRR995042.2x36mers.noMT.bwa.unique.dedup.wig -notitle -uniqueBAM -RPM &
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- LB115_Mu3-CRR995043.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes LB115_Mu3-CRR995043.2x36mers.noMT.bwa.unique.dedup.wig -notitle -uniqueBAM -RPM &
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- LB168_F_Br2-CRR995044.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes LB168_F_Br2-CRR995044.2x36mers.noMT.bwa.unique.dedup.wig -notitle -uniqueBAM -RPM &
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- LB168_F_Li2-CRR995045.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes LB168_F_Li2-CRR995045.2x36mers.noMT.bwa.unique.dedup.wig -notitle -uniqueBAM -RPM &
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- LB168_F_Mu2-CRR995046.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes LB168_F_Mu2-CRR995046.2x36mers.noMT.bwa.unique.dedup.wig -notitle -uniqueBAM -RPM &
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- LB168_G_Br1-CRR995047.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes LB168_G_Br1-CRR995047.2x36mers.noMT.bwa.unique.dedup.wig -notitle -uniqueBAM -RPM &
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- LB168_G_Li1-CRR995048.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes LB168_G_Li1-CRR995048.2x36mers.noMT.bwa.unique.dedup.wig -notitle -uniqueBAM -RPM &
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- LB168_G_Mu1-CRR995049.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes LB168_G_Mu1-CRR995049.2x36mers.noMT.bwa.unique.dedup.wig -notitle -uniqueBAM -RPM &
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- LB168_H_Br3-CRR995050.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes LB168_H_Br3-CRR995050.2x36mers.noMT.bwa.unique.dedup.wig -notitle -uniqueBAM -RPM &
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- LB168_H_Li3-CRR995051.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes LB168_H_Li3-CRR995051.2x36mers.noMT.bwa.unique.dedup.wig -notitle -uniqueBAM -RPM &
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- LB168_H_Mu3-CRR995052.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes LB168_H_Mu3-CRR995052.2x36mers.noMT.bwa.unique.dedup.wig -notitle -uniqueBAM -RPM &
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- LB40_Br1-CRR995053.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes LB40_Br1-CRR995053.2x36mers.noMT.bwa.unique.dedup.wig -notitle -uniqueBAM -RPM &
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- LB40_Br3-CRR995055.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes LB40_Br3-CRR995055.2x36mers.noMT.bwa.unique.dedup.wig -notitle -uniqueBAM -RPM &
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- LB40_Li1-CRR995056.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes LB40_Li1-CRR995056.2x36mers.noMT.bwa.unique.dedup.wig -notitle -uniqueBAM -RPM &
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- LB40_Li2-CRR995057.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes LB40_Li2-CRR995057.2x36mers.noMT.bwa.unique.dedup.wig -notitle -uniqueBAM -RPM &
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- LB40_Li3-CRR995058.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes LB40_Li3-CRR995058.2x36mers.noMT.bwa.unique.dedup.wig -notitle -uniqueBAM -RPM &
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- LB40_Mu2-CRR995060.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes LB40_Mu2-CRR995060.2x36mers.noMT.bwa.unique.dedup.wig -notitle -uniqueBAM -RPM &
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- LB40_Mu3-CRR995061.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes LB40_Mu3-CRR995061.2x36mers.noMT.bwa.unique.dedup.wig -notitle -uniqueBAM -RPM &
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- LB40_Pl1-CRR995062.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes LB40_Pl1-CRR995062.2x36mers.noMT.bwa.unique.dedup.wig -notitle -uniqueBAM -RPM &
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- LB40_Pl2-CRR995063.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes LB40_Pl2-CRR995063.2x36mers.noMT.bwa.unique.dedup.wig -notitle -uniqueBAM -RPM &
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- LB40_Pl3-CRR995064.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes LB40_Pl3-CRR995064.2x36mers.noMT.bwa.unique.dedup.wig -notitle -uniqueBAM -RPM &
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- LB70_Br1-CRR995065.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes LB70_Br1-CRR995065.2x36mers.noMT.bwa.unique.dedup.wig -notitle -uniqueBAM -RPM &
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- LB70_Br2-CRR995066.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes LB70_Br2-CRR995066.2x36mers.noMT.bwa.unique.dedup.wig -notitle -uniqueBAM -RPM &
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- LB70_Br3-CRR995067.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes LB70_Br3-CRR995067.2x36mers.noMT.bwa.unique.dedup.wig -notitle -uniqueBAM -RPM &
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- LB70_Li1-CRR995068.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes LB70_Li1-CRR995068.2x36mers.noMT.bwa.unique.dedup.wig -notitle -uniqueBAM -RPM &
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- LB70_Li2-CRR995069.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes LB70_Li2-CRR995069.2x36mers.noMT.bwa.unique.dedup.wig -notitle -uniqueBAM -RPM &
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- LB70_Li3-CRR995070.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes LB70_Li3-CRR995070.2x36mers.noMT.bwa.unique.dedup.wig -notitle -uniqueBAM -RPM &
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- LB70_Mu1-CRR995071.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes LB70_Mu1-CRR995071.2x36mers.noMT.bwa.unique.dedup.wig -notitle -uniqueBAM -RPM &
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- LB70_Mu2-CRR995072.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes LB70_Mu2-CRR995072.2x36mers.noMT.bwa.unique.dedup.wig -notitle -uniqueBAM -RPM &
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- LB70_Mu3-CRR995073.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes LB70_Mu3-CRR995073.2x36mers.noMT.bwa.unique.dedup.wig -notitle -uniqueBAM -RPM &
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- LB70_Pl1-CRR995074.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes LB70_Pl1-CRR995074.2x36mers.noMT.bwa.unique.dedup.wig -notitle -uniqueBAM -RPM &
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- LB70_Pl2-CRR995075.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes LB70_Pl2-CRR995075.2x36mers.noMT.bwa.unique.dedup.wig -notitle -uniqueBAM -RPM &
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- LB70_Pl3-CRR995076.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes LB70_Pl3-CRR995076.2x36mers.noMT.bwa.unique.dedup.wig -notitle -uniqueBAM -RPM &
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- LS115_Br1-CRR995077.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes LS115_Br1-CRR995077.2x36mers.noMT.bwa.unique.dedup.wig -notitle -uniqueBAM -RPM &
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- LS115_Br2-CRR995078.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes LS115_Br2-CRR995078.2x36mers.noMT.bwa.unique.dedup.wig -notitle -uniqueBAM -RPM &
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- LS115_Br3-CRR995079.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes LS115_Br3-CRR995079.2x36mers.noMT.bwa.unique.dedup.wig -notitle -uniqueBAM -RPM &
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- LS115_Li1-CRR995080.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes LS115_Li1-CRR995080.2x36mers.noMT.bwa.unique.dedup.wig -notitle -uniqueBAM -RPM &
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- LS115_Li2-CRR995081.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes LS115_Li2-CRR995081.2x36mers.noMT.bwa.unique.dedup.wig -notitle -uniqueBAM -RPM &
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- LS115_Li3-CRR995082.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes LS115_Li3-CRR995082.2x36mers.noMT.bwa.unique.dedup.wig -notitle -uniqueBAM -RPM &
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- LS115_Mu1-CRR995083.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes LS115_Mu1-CRR995083.2x36mers.noMT.bwa.unique.dedup.wig -notitle -uniqueBAM -RPM &
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- LS115_Mu2-CRR995084.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes LS115_Mu2-CRR995084.2x36mers.noMT.bwa.unique.dedup.wig -notitle -uniqueBAM -RPM &
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- LS115_Mu3-CRR995085.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes LS115_Mu3-CRR995085.2x36mers.noMT.bwa.unique.dedup.wig -notitle -uniqueBAM -RPM &
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- LS168_B_Li1-CRR995087.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes LS168_B_Li1-CRR995087.2x36mers.noMT.bwa.unique.dedup.wig -notitle -uniqueBAM -RPM &
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- LS168_B_Mu1-CRR995088.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes LS168_B_Mu1-CRR995088.2x36mers.noMT.bwa.unique.dedup.wig -notitle -uniqueBAM -RPM &
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- LS168_C_Br2-CRR995089.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes LS168_C_Br2-CRR995089.2x36mers.noMT.bwa.unique.dedup.wig -notitle -uniqueBAM -RPM &
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- LS168_C_Li2-CRR995090.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes LS168_C_Li2-CRR995090.2x36mers.noMT.bwa.unique.dedup.wig -notitle -uniqueBAM -RPM &
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- LS168_C_Mu2-CRR995091.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes LS168_C_Mu2-CRR995091.2x36mers.noMT.bwa.unique.dedup.wig -notitle -uniqueBAM -RPM &
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- LS168_L_Li3-CRR995092.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes LS168_L_Li3-CRR995092.2x36mers.noMT.bwa.unique.dedup.wig -notitle -uniqueBAM -RPM &
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- LS40_Br2-CRR995095.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes LS40_Br2-CRR995095.2x36mers.noMT.bwa.unique.dedup.wig -notitle -uniqueBAM -RPM &
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- LS40_Br3-CRR995096.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes LS40_Br3-CRR995096.2x36mers.noMT.bwa.unique.dedup.wig -notitle -uniqueBAM -RPM &
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- LS40_Li1-CRR995097.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes LS40_Li1-CRR995097.2x36mers.noMT.bwa.unique.dedup.wig -notitle -uniqueBAM -RPM &
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- LS40_Li2-CRR995098.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes LS40_Li2-CRR995098.2x36mers.noMT.bwa.unique.dedup.wig -notitle -uniqueBAM -RPM &
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- LS40_Li3-CRR995099.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes LS40_Li3-CRR995099.2x36mers.noMT.bwa.unique.dedup.wig -notitle -uniqueBAM -RPM &
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- LS40_Mu1-CRR995100.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes LS40_Mu1-CRR995100.2x36mers.noMT.bwa.unique.dedup.wig -notitle -uniqueBAM -RPM &
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- LS40_Mu2-CRR995101.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes LS40_Mu2-CRR995101.2x36mers.noMT.bwa.unique.dedup.wig -notitle -uniqueBAM -RPM &
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- LS40_Mu3-CRR995102.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes LS40_Mu3-CRR995102.2x36mers.noMT.bwa.unique.dedup.wig -notitle -uniqueBAM -RPM &
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- LS40_Pl1-CRR995103.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes LS40_Pl1-CRR995103.2x36mers.noMT.bwa.unique.dedup.wig -notitle -uniqueBAM -RPM &
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- LS40_Pl2-CRR995104.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes LS40_Pl2-CRR995104.2x36mers.noMT.bwa.unique.dedup.wig -notitle -uniqueBAM -RPM &
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- LS40_Pl3-CRR995105.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes LS40_Pl3-CRR995105.2x36mers.noMT.bwa.unique.dedup.wig -notitle -uniqueBAM -RPM &
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- LS70_Br1-CRR995106.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes LS70_Br1-CRR995106.2x36mers.noMT.bwa.unique.dedup.wig -notitle -uniqueBAM -RPM &
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- LS70_Br2-CRR995107.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes LS70_Br2-CRR995107.2x36mers.noMT.bwa.unique.dedup.wig -notitle -uniqueBAM -RPM &
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- LS70_Br3-CRR995108.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes LS70_Br3-CRR995108.2x36mers.noMT.bwa.unique.dedup.wig -notitle -uniqueBAM -RPM &
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- LS70_Li1-CRR995109.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes LS70_Li1-CRR995109.2x36mers.noMT.bwa.unique.dedup.wig -notitle -uniqueBAM -RPM &
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- LS70_Li2-CRR995110.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes LS70_Li2-CRR995110.2x36mers.noMT.bwa.unique.dedup.wig -notitle -uniqueBAM -RPM &
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- LS70_Li3-CRR995111.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes LS70_Li3-CRR995111.2x36mers.noMT.bwa.unique.dedup.wig -notitle -uniqueBAM -RPM &
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- LS70_Mu1-CRR995112.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes LS70_Mu1-CRR995112.2x36mers.noMT.bwa.unique.dedup.wig -notitle -uniqueBAM -RPM &
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- LS70_Mu2-CRR995113.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes LS70_Mu2-CRR995113.2x36mers.noMT.bwa.unique.dedup.wig -notitle -uniqueBAM -RPM &
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- LS70_Mu3-CRR995114.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes LS70_Mu3-CRR995114.2x36mers.noMT.bwa.unique.dedup.wig -notitle -uniqueBAM -RPM &
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- LS70_Pl2-CRR995115.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes LS70_Pl2-CRR995115.2x36mers.noMT.bwa.unique.dedup.wig -notitle -uniqueBAM -RPM &
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- LS70_Pl3-CRR995116.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes LS70_Pl3-CRR995116.2x36mers.noMT.bwa.unique.dedup.wig -notitle -uniqueBAM -RPM &
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.py --- DB115_Br2-CRR994956.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes DB115_Br2-CRR994956.2x36mers.noMT.bwa.unique.dedup.5p.counts.wig -notitle -uniqueBAM -shift 4 &
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.py --- DB115_Br3-CRR994957.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes DB115_Br3-CRR994957.2x36mers.noMT.bwa.unique.dedup.5p.counts.wig -notitle -uniqueBAM -shift 4 &
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.py --- DB115_Li2-CRR994959.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes DB115_Li2-CRR994959.2x36mers.noMT.bwa.unique.dedup.5p.counts.wig -notitle -uniqueBAM -shift 4 &
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.py --- DB115_Li3-CRR994960.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes DB115_Li3-CRR994960.2x36mers.noMT.bwa.unique.dedup.5p.counts.wig -notitle -uniqueBAM -shift 4 &
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.py --- DB115_Mu1-CRR994961.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes DB115_Mu1-CRR994961.2x36mers.noMT.bwa.unique.dedup.5p.counts.wig -notitle -uniqueBAM -shift 4 &
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.py --- DB115_Mu2-CRR994962.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes DB115_Mu2-CRR994962.2x36mers.noMT.bwa.unique.dedup.5p.counts.wig -notitle -uniqueBAM -shift 4 &
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.py --- DB115_Mu3-CRR994963.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes DB115_Mu3-CRR994963.2x36mers.noMT.bwa.unique.dedup.5p.counts.wig -notitle -uniqueBAM -shift 4 &
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.py --- DB168_E_Br1-CRR994964.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes DB168_E_Br1-CRR994964.2x36mers.noMT.bwa.unique.dedup.5p.counts.wig -notitle -uniqueBAM -shift 4 &
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.py --- DB168_E_Li1-CRR994965.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes DB168_E_Li1-CRR994965.2x36mers.noMT.bwa.unique.dedup.5p.counts.wig -notitle -uniqueBAM -shift 4 &
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.py --- DB168_I_Br2-CRR994967.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes DB168_I_Br2-CRR994967.2x36mers.noMT.bwa.unique.dedup.5p.counts.wig -notitle -uniqueBAM -shift 4 &
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.py --- DB168_I_Li2-CRR994968.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes DB168_I_Li2-CRR994968.2x36mers.noMT.bwa.unique.dedup.5p.counts.wig -notitle -uniqueBAM -shift 4 &
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.py --- DB168_I_Mu2-CRR994969.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes DB168_I_Mu2-CRR994969.2x36mers.noMT.bwa.unique.dedup.5p.counts.wig -notitle -uniqueBAM -shift 4 &
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.py --- DB168_J_Br3-CRR994970.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes DB168_J_Br3-CRR994970.2x36mers.noMT.bwa.unique.dedup.5p.counts.wig -notitle -uniqueBAM -shift 4 &
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.py --- DB168_J_Li3-CRR994971.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes DB168_J_Li3-CRR994971.2x36mers.noMT.bwa.unique.dedup.5p.counts.wig -notitle -uniqueBAM -shift 4 &
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.py --- DB168_J_Mu3-CRR994972.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes DB168_J_Mu3-CRR994972.2x36mers.noMT.bwa.unique.dedup.5p.counts.wig -notitle -uniqueBAM -shift 4 &
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.py --- DB40_Br1-CRR994973.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes DB40_Br1-CRR994973.2x36mers.noMT.bwa.unique.dedup.5p.counts.wig -notitle -uniqueBAM -shift 4 &
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.py --- DB40_Li1-CRR994976.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes DB40_Li1-CRR994976.2x36mers.noMT.bwa.unique.dedup.5p.counts.wig -notitle -uniqueBAM -shift 4 &
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.py --- DB40_Li2-CRR994977.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes DB40_Li2-CRR994977.2x36mers.noMT.bwa.unique.dedup.5p.counts.wig -notitle -uniqueBAM -shift 4 &
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.py --- DB40_Li3-CRR994978.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes DB40_Li3-CRR994978.2x36mers.noMT.bwa.unique.dedup.5p.counts.wig -notitle -uniqueBAM -shift 4 &
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.py --- DB40_Mu1-CRR994979.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes DB40_Mu1-CRR994979.2x36mers.noMT.bwa.unique.dedup.5p.counts.wig -notitle -uniqueBAM -shift 4 &
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.py --- DB40_Mu2-CRR994980.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes DB40_Mu2-CRR994980.2x36mers.noMT.bwa.unique.dedup.5p.counts.wig -notitle -uniqueBAM -shift 4 &
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.py --- DB40_Mu3-CRR994981.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes DB40_Mu3-CRR994981.2x36mers.noMT.bwa.unique.dedup.5p.counts.wig -notitle -uniqueBAM -shift 4 &
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.py --- DB40_Pl1-CRR994982.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes DB40_Pl1-CRR994982.2x36mers.noMT.bwa.unique.dedup.5p.counts.wig -notitle -uniqueBAM -shift 4 &
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.py --- DB40_Pl2-CRR994983.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes DB40_Pl2-CRR994983.2x36mers.noMT.bwa.unique.dedup.5p.counts.wig -notitle -uniqueBAM -shift 4 &
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.py --- DB40_Pl3-CRR994984.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes DB40_Pl3-CRR994984.2x36mers.noMT.bwa.unique.dedup.5p.counts.wig -notitle -uniqueBAM -shift 4 &
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.py --- DB70_Br1-CRR994985.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes DB70_Br1-CRR994985.2x36mers.noMT.bwa.unique.dedup.5p.counts.wig -notitle -uniqueBAM -shift 4 &
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.py --- DB70_Br3-CRR994987.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes DB70_Br3-CRR994987.2x36mers.noMT.bwa.unique.dedup.5p.counts.wig -notitle -uniqueBAM -shift 4 &
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.py --- DB70_Li2-CRR994989.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes DB70_Li2-CRR994989.2x36mers.noMT.bwa.unique.dedup.5p.counts.wig -notitle -uniqueBAM -shift 4 &
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.py --- DB70_Li3-CRR994990.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes DB70_Li3-CRR994990.2x36mers.noMT.bwa.unique.dedup.5p.counts.wig -notitle -uniqueBAM -shift 4 &
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.py --- DB70_Mu1-CRR994991.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes DB70_Mu1-CRR994991.2x36mers.noMT.bwa.unique.dedup.5p.counts.wig -notitle -uniqueBAM -shift 4 &
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.py --- DB70_Mu2-CRR994992.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes DB70_Mu2-CRR994992.2x36mers.noMT.bwa.unique.dedup.5p.counts.wig -notitle -uniqueBAM -shift 4 &
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.py --- DB70_Mu3-CRR994993.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes DB70_Mu3-CRR994993.2x36mers.noMT.bwa.unique.dedup.5p.counts.wig -notitle -uniqueBAM -shift 4 &
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.py --- DB70_Pl1-CRR994994.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes DB70_Pl1-CRR994994.2x36mers.noMT.bwa.unique.dedup.5p.counts.wig -notitle -uniqueBAM -shift 4 &
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.py --- DS115_Br1-CRR994995.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes DS115_Br1-CRR994995.2x36mers.noMT.bwa.unique.dedup.5p.counts.wig -notitle -uniqueBAM -shift 4 &
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.py --- DS115_Br2-CRR994996.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes DS115_Br2-CRR994996.2x36mers.noMT.bwa.unique.dedup.5p.counts.wig -notitle -uniqueBAM -shift 4 &
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.py --- DS115_Br3-CRR994997.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes DS115_Br3-CRR994997.2x36mers.noMT.bwa.unique.dedup.5p.counts.wig -notitle -uniqueBAM -shift 4 &
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.py --- DS115_Li1-CRR994998.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes DS115_Li1-CRR994998.2x36mers.noMT.bwa.unique.dedup.5p.counts.wig -notitle -uniqueBAM -shift 4 &
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.py --- DS115_Li2-CRR994999.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes DS115_Li2-CRR994999.2x36mers.noMT.bwa.unique.dedup.5p.counts.wig -notitle -uniqueBAM -shift 4 &
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.py --- DS115_Li3-CRR995000.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes DS115_Li3-CRR995000.2x36mers.noMT.bwa.unique.dedup.5p.counts.wig -notitle -uniqueBAM -shift 4 &
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.py --- DS115_Mu1-CRR995001.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes DS115_Mu1-CRR995001.2x36mers.noMT.bwa.unique.dedup.5p.counts.wig -notitle -uniqueBAM -shift 4 &
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.py --- DS115_Mu2-CRR995002.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes DS115_Mu2-CRR995002.2x36mers.noMT.bwa.unique.dedup.5p.counts.wig -notitle -uniqueBAM -shift 4 &
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.py --- DS115_Mu3-CRR995003.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes DS115_Mu3-CRR995003.2x36mers.noMT.bwa.unique.dedup.5p.counts.wig -notitle -uniqueBAM -shift 4 &
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.py --- DS168_M_Br1-CRR995004.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes DS168_M_Br1-CRR995004.2x36mers.noMT.bwa.unique.dedup.5p.counts.wig -notitle -uniqueBAM -shift 4 &
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.py --- DS168_M_Li1-CRR995005.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes DS168_M_Li1-CRR995005.2x36mers.noMT.bwa.unique.dedup.5p.counts.wig -notitle -uniqueBAM -shift 4 &
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.py --- DS168_N_Br2-CRR995007.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes DS168_N_Br2-CRR995007.2x36mers.noMT.bwa.unique.dedup.5p.counts.wig -notitle -uniqueBAM -shift 4 &
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.py --- DS168_N_Li2-CRR995008.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes DS168_N_Li2-CRR995008.2x36mers.noMT.bwa.unique.dedup.5p.counts.wig -notitle -uniqueBAM -shift 4 &
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.py --- DS168_N_Mu2-CRR995009.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes DS168_N_Mu2-CRR995009.2x36mers.noMT.bwa.unique.dedup.5p.counts.wig -notitle -uniqueBAM -shift 4 &
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.py --- DS168_O_Br3-CRR995010.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes DS168_O_Br3-CRR995010.2x36mers.noMT.bwa.unique.dedup.5p.counts.wig -notitle -uniqueBAM -shift 4 &
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.py --- DS168_O_Li3-CRR995011.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes DS168_O_Li3-CRR995011.2x36mers.noMT.bwa.unique.dedup.5p.counts.wig -notitle -uniqueBAM -shift 4 &
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.py --- DS40_Br1-CRR995013.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes DS40_Br1-CRR995013.2x36mers.noMT.bwa.unique.dedup.5p.counts.wig -notitle -uniqueBAM -shift 4 &
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.py --- DS40_Br2-CRR995014.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes DS40_Br2-CRR995014.2x36mers.noMT.bwa.unique.dedup.5p.counts.wig -notitle -uniqueBAM -shift 4 &
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.py --- DS40_Br3-CRR995015.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes DS40_Br3-CRR995015.2x36mers.noMT.bwa.unique.dedup.5p.counts.wig -notitle -uniqueBAM -shift 4 &
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.py --- DS40_Li2-CRR995016.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes DS40_Li2-CRR995016.2x36mers.noMT.bwa.unique.dedup.5p.counts.wig -notitle -uniqueBAM -shift 4 &
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.py --- DS40_Li3-CRR995017.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes DS40_Li3-CRR995017.2x36mers.noMT.bwa.unique.dedup.5p.counts.wig -notitle -uniqueBAM -shift 4 &
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.py --- DS40_Mu1-CRR995018.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes DS40_Mu1-CRR995018.2x36mers.noMT.bwa.unique.dedup.5p.counts.wig -notitle -uniqueBAM -shift 4 &
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.py --- DS40_Mu2-CRR995019.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes DS40_Mu2-CRR995019.2x36mers.noMT.bwa.unique.dedup.5p.counts.wig -notitle -uniqueBAM -shift 4 &
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.py --- DS40_Mu3-CRR995020.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes DS40_Mu3-CRR995020.2x36mers.noMT.bwa.unique.dedup.5p.counts.wig -notitle -uniqueBAM -shift 4 &
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.py --- DS40_Pl1-CRR995021.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes DS40_Pl1-CRR995021.2x36mers.noMT.bwa.unique.dedup.5p.counts.wig -notitle -uniqueBAM -shift 4 &
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.py --- DS40_Pl2-CRR995022.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes DS40_Pl2-CRR995022.2x36mers.noMT.bwa.unique.dedup.5p.counts.wig -notitle -uniqueBAM -shift 4 &
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.py --- DS40_Pl3-CRR995023.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes DS40_Pl3-CRR995023.2x36mers.noMT.bwa.unique.dedup.5p.counts.wig -notitle -uniqueBAM -shift 4 &
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.py --- DS70_Br1-CRR995024.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes DS70_Br1-CRR995024.2x36mers.noMT.bwa.unique.dedup.5p.counts.wig -notitle -uniqueBAM -shift 4 &
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.py --- DS70_Br2-CRR995025.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes DS70_Br2-CRR995025.2x36mers.noMT.bwa.unique.dedup.5p.counts.wig -notitle -uniqueBAM -shift 4 &
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.py --- DS70_Br3-CRR995026.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes DS70_Br3-CRR995026.2x36mers.noMT.bwa.unique.dedup.5p.counts.wig -notitle -uniqueBAM -shift 4 &
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.py --- DS70_Li1-CRR995027.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes DS70_Li1-CRR995027.2x36mers.noMT.bwa.unique.dedup.5p.counts.wig -notitle -uniqueBAM -shift 4 &
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.py --- DS70_Li2-CRR995028.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes DS70_Li2-CRR995028.2x36mers.noMT.bwa.unique.dedup.5p.counts.wig -notitle -uniqueBAM -shift 4 &
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.py --- DS70_Li3-CRR995029.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes DS70_Li3-CRR995029.2x36mers.noMT.bwa.unique.dedup.5p.counts.wig -notitle -uniqueBAM -shift 4 &
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.py --- DS70_Mu1-CRR995030.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes DS70_Mu1-CRR995030.2x36mers.noMT.bwa.unique.dedup.5p.counts.wig -notitle -uniqueBAM -shift 4 &
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.py --- DS70_Mu2-CRR995031.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes DS70_Mu2-CRR995031.2x36mers.noMT.bwa.unique.dedup.5p.counts.wig -notitle -uniqueBAM -shift 4 &
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.py --- DS70_Mu3-CRR995032.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes DS70_Mu3-CRR995032.2x36mers.noMT.bwa.unique.dedup.5p.counts.wig -notitle -uniqueBAM -shift 4 &
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.py --- DS70_Pl1-CRR995033.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes DS70_Pl1-CRR995033.2x36mers.noMT.bwa.unique.dedup.5p.counts.wig -notitle -uniqueBAM -shift 4 &
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.py --- DS70_Pl3-CRR995034.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes DS70_Pl3-CRR995034.2x36mers.noMT.bwa.unique.dedup.5p.counts.wig -notitle -uniqueBAM -shift 4 &
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.py --- LB115_Br1-CRR995035.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes LB115_Br1-CRR995035.2x36mers.noMT.bwa.unique.dedup.5p.counts.wig -notitle -uniqueBAM -shift 4 &
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.py --- LB115_Br2-CRR995036.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes LB115_Br2-CRR995036.2x36mers.noMT.bwa.unique.dedup.5p.counts.wig -notitle -uniqueBAM -shift 4 &
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.py --- LB115_Br3-CRR995037.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes LB115_Br3-CRR995037.2x36mers.noMT.bwa.unique.dedup.5p.counts.wig -notitle -uniqueBAM -shift 4 &
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.py --- LB115_Li1-CRR995038.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes LB115_Li1-CRR995038.2x36mers.noMT.bwa.unique.dedup.5p.counts.wig -notitle -uniqueBAM -shift 4 &
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.py --- LB115_Li2-CRR995039.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes LB115_Li2-CRR995039.2x36mers.noMT.bwa.unique.dedup.5p.counts.wig -notitle -uniqueBAM -shift 4 &
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.py --- LB115_Li3-CRR995040.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes LB115_Li3-CRR995040.2x36mers.noMT.bwa.unique.dedup.5p.counts.wig -notitle -uniqueBAM -shift 4 &
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.py --- LB115_Mu1-CRR995041.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes LB115_Mu1-CRR995041.2x36mers.noMT.bwa.unique.dedup.5p.counts.wig -notitle -uniqueBAM -shift 4 &
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.py --- LB115_Mu2-CRR995042.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes LB115_Mu2-CRR995042.2x36mers.noMT.bwa.unique.dedup.5p.counts.wig -notitle -uniqueBAM -shift 4 &
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.py --- LB115_Mu3-CRR995043.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes LB115_Mu3-CRR995043.2x36mers.noMT.bwa.unique.dedup.5p.counts.wig -notitle -uniqueBAM -shift 4 &
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.py --- LB168_F_Br2-CRR995044.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes LB168_F_Br2-CRR995044.2x36mers.noMT.bwa.unique.dedup.5p.counts.wig -notitle -uniqueBAM -shift 4 &
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.py --- LB168_F_Li2-CRR995045.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes LB168_F_Li2-CRR995045.2x36mers.noMT.bwa.unique.dedup.5p.counts.wig -notitle -uniqueBAM -shift 4 &
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.py --- LB168_F_Mu2-CRR995046.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes LB168_F_Mu2-CRR995046.2x36mers.noMT.bwa.unique.dedup.5p.counts.wig -notitle -uniqueBAM -shift 4 &
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.py --- LB168_G_Br1-CRR995047.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes LB168_G_Br1-CRR995047.2x36mers.noMT.bwa.unique.dedup.5p.counts.wig -notitle -uniqueBAM -shift 4 &
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.py --- LB168_G_Li1-CRR995048.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes LB168_G_Li1-CRR995048.2x36mers.noMT.bwa.unique.dedup.5p.counts.wig -notitle -uniqueBAM -shift 4 &
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.py --- LB168_G_Mu1-CRR995049.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes LB168_G_Mu1-CRR995049.2x36mers.noMT.bwa.unique.dedup.5p.counts.wig -notitle -uniqueBAM -shift 4 &
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.py --- LB168_H_Br3-CRR995050.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes LB168_H_Br3-CRR995050.2x36mers.noMT.bwa.unique.dedup.5p.counts.wig -notitle -uniqueBAM -shift 4 &
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.py --- LB168_H_Li3-CRR995051.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes LB168_H_Li3-CRR995051.2x36mers.noMT.bwa.unique.dedup.5p.counts.wig -notitle -uniqueBAM -shift 4 &
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.py --- LB168_H_Mu3-CRR995052.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes LB168_H_Mu3-CRR995052.2x36mers.noMT.bwa.unique.dedup.5p.counts.wig -notitle -uniqueBAM -shift 4 &
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.py --- LB40_Br1-CRR995053.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes LB40_Br1-CRR995053.2x36mers.noMT.bwa.unique.dedup.5p.counts.wig -notitle -uniqueBAM -shift 4 &
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.py --- LB40_Br3-CRR995055.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes LB40_Br3-CRR995055.2x36mers.noMT.bwa.unique.dedup.5p.counts.wig -notitle -uniqueBAM -shift 4 &
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.py --- LB40_Li1-CRR995056.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes LB40_Li1-CRR995056.2x36mers.noMT.bwa.unique.dedup.5p.counts.wig -notitle -uniqueBAM -shift 4 &
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.py --- LB40_Li2-CRR995057.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes LB40_Li2-CRR995057.2x36mers.noMT.bwa.unique.dedup.5p.counts.wig -notitle -uniqueBAM -shift 4 &
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.py --- LB40_Li3-CRR995058.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes LB40_Li3-CRR995058.2x36mers.noMT.bwa.unique.dedup.5p.counts.wig -notitle -uniqueBAM -shift 4 &
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.py --- LB40_Mu2-CRR995060.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes LB40_Mu2-CRR995060.2x36mers.noMT.bwa.unique.dedup.5p.counts.wig -notitle -uniqueBAM -shift 4 &
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.py --- LB40_Mu3-CRR995061.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes LB40_Mu3-CRR995061.2x36mers.noMT.bwa.unique.dedup.5p.counts.wig -notitle -uniqueBAM -shift 4 &
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.py --- LB40_Pl1-CRR995062.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes LB40_Pl1-CRR995062.2x36mers.noMT.bwa.unique.dedup.5p.counts.wig -notitle -uniqueBAM -shift 4 &
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.py --- LB40_Pl2-CRR995063.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes LB40_Pl2-CRR995063.2x36mers.noMT.bwa.unique.dedup.5p.counts.wig -notitle -uniqueBAM -shift 4 &
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.py --- LB40_Pl3-CRR995064.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes LB40_Pl3-CRR995064.2x36mers.noMT.bwa.unique.dedup.5p.counts.wig -notitle -uniqueBAM -shift 4 &
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.py --- LB70_Br1-CRR995065.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes LB70_Br1-CRR995065.2x36mers.noMT.bwa.unique.dedup.5p.counts.wig -notitle -uniqueBAM -shift 4 &
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.py --- LB70_Br2-CRR995066.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes LB70_Br2-CRR995066.2x36mers.noMT.bwa.unique.dedup.5p.counts.wig -notitle -uniqueBAM -shift 4 &
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.py --- LB70_Br3-CRR995067.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes LB70_Br3-CRR995067.2x36mers.noMT.bwa.unique.dedup.5p.counts.wig -notitle -uniqueBAM -shift 4 &
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.py --- LB70_Li1-CRR995068.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes LB70_Li1-CRR995068.2x36mers.noMT.bwa.unique.dedup.5p.counts.wig -notitle -uniqueBAM -shift 4 &
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.py --- LB70_Li2-CRR995069.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes LB70_Li2-CRR995069.2x36mers.noMT.bwa.unique.dedup.5p.counts.wig -notitle -uniqueBAM -shift 4 &
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.py --- LB70_Li3-CRR995070.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes LB70_Li3-CRR995070.2x36mers.noMT.bwa.unique.dedup.5p.counts.wig -notitle -uniqueBAM -shift 4 &
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.py --- LB70_Mu1-CRR995071.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes LB70_Mu1-CRR995071.2x36mers.noMT.bwa.unique.dedup.5p.counts.wig -notitle -uniqueBAM -shift 4 &
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.py --- LB70_Mu2-CRR995072.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes LB70_Mu2-CRR995072.2x36mers.noMT.bwa.unique.dedup.5p.counts.wig -notitle -uniqueBAM -shift 4 &
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.py --- LB70_Mu3-CRR995073.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes LB70_Mu3-CRR995073.2x36mers.noMT.bwa.unique.dedup.5p.counts.wig -notitle -uniqueBAM -shift 4 &
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.py --- LB70_Pl1-CRR995074.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes LB70_Pl1-CRR995074.2x36mers.noMT.bwa.unique.dedup.5p.counts.wig -notitle -uniqueBAM -shift 4 &
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.py --- LB70_Pl2-CRR995075.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes LB70_Pl2-CRR995075.2x36mers.noMT.bwa.unique.dedup.5p.counts.wig -notitle -uniqueBAM -shift 4 &
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.py --- LB70_Pl3-CRR995076.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes LB70_Pl3-CRR995076.2x36mers.noMT.bwa.unique.dedup.5p.counts.wig -notitle -uniqueBAM -shift 4 &
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.py --- LS115_Br1-CRR995077.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes LS115_Br1-CRR995077.2x36mers.noMT.bwa.unique.dedup.5p.counts.wig -notitle -uniqueBAM -shift 4 &
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.py --- LS115_Br2-CRR995078.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes LS115_Br2-CRR995078.2x36mers.noMT.bwa.unique.dedup.5p.counts.wig -notitle -uniqueBAM -shift 4 &
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.py --- LS115_Br3-CRR995079.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes LS115_Br3-CRR995079.2x36mers.noMT.bwa.unique.dedup.5p.counts.wig -notitle -uniqueBAM -shift 4 &
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.py --- LS115_Li1-CRR995080.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes LS115_Li1-CRR995080.2x36mers.noMT.bwa.unique.dedup.5p.counts.wig -notitle -uniqueBAM -shift 4 &
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.py --- LS115_Li2-CRR995081.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes LS115_Li2-CRR995081.2x36mers.noMT.bwa.unique.dedup.5p.counts.wig -notitle -uniqueBAM -shift 4 &
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.py --- LS115_Li3-CRR995082.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes LS115_Li3-CRR995082.2x36mers.noMT.bwa.unique.dedup.5p.counts.wig -notitle -uniqueBAM -shift 4 &
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.py --- LS115_Mu1-CRR995083.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes LS115_Mu1-CRR995083.2x36mers.noMT.bwa.unique.dedup.5p.counts.wig -notitle -uniqueBAM -shift 4 &
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.py --- LS115_Mu2-CRR995084.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes LS115_Mu2-CRR995084.2x36mers.noMT.bwa.unique.dedup.5p.counts.wig -notitle -uniqueBAM -shift 4 &
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.py --- LS115_Mu3-CRR995085.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes LS115_Mu3-CRR995085.2x36mers.noMT.bwa.unique.dedup.5p.counts.wig -notitle -uniqueBAM -shift 4 &
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.py --- LS168_B_Li1-CRR995087.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes LS168_B_Li1-CRR995087.2x36mers.noMT.bwa.unique.dedup.5p.counts.wig -notitle -uniqueBAM -shift 4 &
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.py --- LS168_B_Mu1-CRR995088.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes LS168_B_Mu1-CRR995088.2x36mers.noMT.bwa.unique.dedup.5p.counts.wig -notitle -uniqueBAM -shift 4 &
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.py --- LS168_C_Br2-CRR995089.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes LS168_C_Br2-CRR995089.2x36mers.noMT.bwa.unique.dedup.5p.counts.wig -notitle -uniqueBAM -shift 4 &
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.py --- LS168_C_Li2-CRR995090.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes LS168_C_Li2-CRR995090.2x36mers.noMT.bwa.unique.dedup.5p.counts.wig -notitle -uniqueBAM -shift 4 &
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.py --- LS168_C_Mu2-CRR995091.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes LS168_C_Mu2-CRR995091.2x36mers.noMT.bwa.unique.dedup.5p.counts.wig -notitle -uniqueBAM -shift 4 &
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.py --- LS168_L_Li3-CRR995092.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes LS168_L_Li3-CRR995092.2x36mers.noMT.bwa.unique.dedup.5p.counts.wig -notitle -uniqueBAM -shift 4 &
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.py --- LS40_Br2-CRR995095.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes LS40_Br2-CRR995095.2x36mers.noMT.bwa.unique.dedup.5p.counts.wig -notitle -uniqueBAM -shift 4 &
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.py --- LS40_Br3-CRR995096.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes LS40_Br3-CRR995096.2x36mers.noMT.bwa.unique.dedup.5p.counts.wig -notitle -uniqueBAM -shift 4 &
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.py --- LS40_Li1-CRR995097.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes LS40_Li1-CRR995097.2x36mers.noMT.bwa.unique.dedup.5p.counts.wig -notitle -uniqueBAM -shift 4 &
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.py --- LS40_Li2-CRR995098.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes LS40_Li2-CRR995098.2x36mers.noMT.bwa.unique.dedup.5p.counts.wig -notitle -uniqueBAM -shift 4 &
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.py --- LS40_Li3-CRR995099.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes LS40_Li3-CRR995099.2x36mers.noMT.bwa.unique.dedup.5p.counts.wig -notitle -uniqueBAM -shift 4 &
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.py --- LS40_Mu1-CRR995100.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes LS40_Mu1-CRR995100.2x36mers.noMT.bwa.unique.dedup.5p.counts.wig -notitle -uniqueBAM -shift 4 &
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.py --- LS40_Mu2-CRR995101.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes LS40_Mu2-CRR995101.2x36mers.noMT.bwa.unique.dedup.5p.counts.wig -notitle -uniqueBAM -shift 4 &
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.py --- LS40_Mu3-CRR995102.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes LS40_Mu3-CRR995102.2x36mers.noMT.bwa.unique.dedup.5p.counts.wig -notitle -uniqueBAM -shift 4 &
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.py --- LS40_Pl1-CRR995103.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes LS40_Pl1-CRR995103.2x36mers.noMT.bwa.unique.dedup.5p.counts.wig -notitle -uniqueBAM -shift 4 &
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.py --- LS40_Pl2-CRR995104.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes LS40_Pl2-CRR995104.2x36mers.noMT.bwa.unique.dedup.5p.counts.wig -notitle -uniqueBAM -shift 4 &
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.py --- LS40_Pl3-CRR995105.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes LS40_Pl3-CRR995105.2x36mers.noMT.bwa.unique.dedup.5p.counts.wig -notitle -uniqueBAM -shift 4 &
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.py --- LS70_Br1-CRR995106.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes LS70_Br1-CRR995106.2x36mers.noMT.bwa.unique.dedup.5p.counts.wig -notitle -uniqueBAM -shift 4 &
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.py --- LS70_Br2-CRR995107.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes LS70_Br2-CRR995107.2x36mers.noMT.bwa.unique.dedup.5p.counts.wig -notitle -uniqueBAM -shift 4 &
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.py --- LS70_Br3-CRR995108.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes LS70_Br3-CRR995108.2x36mers.noMT.bwa.unique.dedup.5p.counts.wig -notitle -uniqueBAM -shift 4 &
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.py --- LS70_Li1-CRR995109.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes LS70_Li1-CRR995109.2x36mers.noMT.bwa.unique.dedup.5p.counts.wig -notitle -uniqueBAM -shift 4 &
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.py --- LS70_Li2-CRR995110.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes LS70_Li2-CRR995110.2x36mers.noMT.bwa.unique.dedup.5p.counts.wig -notitle -uniqueBAM -shift 4 &
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.py --- LS70_Li3-CRR995111.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes LS70_Li3-CRR995111.2x36mers.noMT.bwa.unique.dedup.5p.counts.wig -notitle -uniqueBAM -shift 4 &
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.py --- LS70_Mu1-CRR995112.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes LS70_Mu1-CRR995112.2x36mers.noMT.bwa.unique.dedup.5p.counts.wig -notitle -uniqueBAM -shift 4 &
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.py --- LS70_Mu2-CRR995113.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes LS70_Mu2-CRR995113.2x36mers.noMT.bwa.unique.dedup.5p.counts.wig -notitle -uniqueBAM -shift 4 &
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.py --- LS70_Mu3-CRR995114.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes LS70_Mu3-CRR995114.2x36mers.noMT.bwa.unique.dedup.5p.counts.wig -notitle -uniqueBAM -shift 4 &
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.py --- LS70_Pl2-CRR995115.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes LS70_Pl2-CRR995115.2x36mers.noMT.bwa.unique.dedup.5p.counts.wig -notitle -uniqueBAM -shift 4 &
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.py --- LS70_Pl3-CRR995116.2x36mers.noMT.bwa.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes LS70_Pl3-CRR995116.2x36mers.noMT.bwa.unique.dedup.5p.counts.wig -notitle -uniqueBAM -shift 4 &