python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py 2025-09-29-DNA-LHG_250822_L01_exp250213_MS8_SCD_gDNA.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-2025-09-29-DNA-LHG_250822_L01_exp250213_MS8_SCD_gDNA.1x36mers.sacCer3.unique.nochrM -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py 2025-09-29-DNA-LHG_250822_L01_exp250213_MS8_SCD_gDNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2025-09-29-DNA-LHG_250822_L01_exp250213_MS8_SCD_gDNA.2x36mers.sacCer3 -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py 2025-09-29-DNA-LHG_250822_L01_exp250213_MS8_SCD_gDNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2025-09-29-DNA-LHG_250822_L01_exp250213_MS8_SCD_gDNA.2x36mers.sacCer3.nochrM.ERMTOC -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -excludeReadsMappingToOtherChromosomes
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py 2025-09-29-DNA-LHG_250822_L01_exp250213_MS8_SCD_gDNA.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-2025-09-29-DNA-LHG_250822_L01_exp250213_MS8_SCD_gDNA.1x36mers.C_glabrata_CBS138_current_chromosomes.unique.nochrM -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py 2025-09-29-DNA-LHG_250822_L01_exp250213_MS8_SCD_gDNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2025-09-29-DNA-LHG_250822_L01_exp250213_MS8_SCD_gDNA.2x36mers.C_glabrata_CBS138_current_chromosomes -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py 2025-09-29-DNA-LHG_250822_L01_exp250213_MS8_SCD_gDNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2025-09-29-DNA-LHG_250822_L01_exp250213_MS8_SCD_gDNA.2x36mers.C_glabrata_CBS138_current_chromosomes.nochrM.ERMTOC -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -excludeReadsMappingToOtherChromosomes
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py 2025-09-29-DNA-LHG_250822_L02_exp250213_MS8_SCGE_gDNA.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-2025-09-29-DNA-LHG_250822_L02_exp250213_MS8_SCGE_gDNA.1x36mers.sacCer3.unique.nochrM -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py 2025-09-29-DNA-LHG_250822_L02_exp250213_MS8_SCGE_gDNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2025-09-29-DNA-LHG_250822_L02_exp250213_MS8_SCGE_gDNA.2x36mers.sacCer3 -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py 2025-09-29-DNA-LHG_250822_L02_exp250213_MS8_SCGE_gDNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2025-09-29-DNA-LHG_250822_L02_exp250213_MS8_SCGE_gDNA.2x36mers.sacCer3.nochrM.ERMTOC -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -excludeReadsMappingToOtherChromosomes
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py 2025-09-29-DNA-LHG_250822_L02_exp250213_MS8_SCGE_gDNA.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-2025-09-29-DNA-LHG_250822_L02_exp250213_MS8_SCGE_gDNA.1x36mers.C_glabrata_CBS138_current_chromosomes.unique.nochrM -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py 2025-09-29-DNA-LHG_250822_L02_exp250213_MS8_SCGE_gDNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2025-09-29-DNA-LHG_250822_L02_exp250213_MS8_SCGE_gDNA.2x36mers.C_glabrata_CBS138_current_chromosomes -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py 2025-09-29-DNA-LHG_250822_L02_exp250213_MS8_SCGE_gDNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2025-09-29-DNA-LHG_250822_L02_exp250213_MS8_SCGE_gDNA.2x36mers.C_glabrata_CBS138_current_chromosomes.nochrM.ERMTOC -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -excludeReadsMappingToOtherChromosomes
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py 2025-09-29-DNA-LHG_250822_L03_exp250213_MS8_SCD_switch_gDNA.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-2025-09-29-DNA-LHG_250822_L03_exp250213_MS8_SCD_switch_gDNA.1x36mers.sacCer3.unique.nochrM -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py 2025-09-29-DNA-LHG_250822_L03_exp250213_MS8_SCD_switch_gDNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2025-09-29-DNA-LHG_250822_L03_exp250213_MS8_SCD_switch_gDNA.2x36mers.sacCer3 -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py 2025-09-29-DNA-LHG_250822_L03_exp250213_MS8_SCD_switch_gDNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2025-09-29-DNA-LHG_250822_L03_exp250213_MS8_SCD_switch_gDNA.2x36mers.sacCer3.nochrM.ERMTOC -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -excludeReadsMappingToOtherChromosomes
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py 2025-09-29-DNA-LHG_250822_L03_exp250213_MS8_SCD_switch_gDNA.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-2025-09-29-DNA-LHG_250822_L03_exp250213_MS8_SCD_switch_gDNA.1x36mers.C_glabrata_CBS138_current_chromosomes.unique.nochrM -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py 2025-09-29-DNA-LHG_250822_L03_exp250213_MS8_SCD_switch_gDNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2025-09-29-DNA-LHG_250822_L03_exp250213_MS8_SCD_switch_gDNA.2x36mers.C_glabrata_CBS138_current_chromosomes -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py 2025-09-29-DNA-LHG_250822_L03_exp250213_MS8_SCD_switch_gDNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2025-09-29-DNA-LHG_250822_L03_exp250213_MS8_SCD_switch_gDNA.2x36mers.C_glabrata_CBS138_current_chromosomes.nochrM.ERMTOC -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -excludeReadsMappingToOtherChromosomes
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py 2025-09-29-DNA-LHG_250822_L04_exp250213_MS8_SCGE_switch_gDNA.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-2025-09-29-DNA-LHG_250822_L04_exp250213_MS8_SCGE_switch_gDNA.1x36mers.sacCer3.unique.nochrM -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py 2025-09-29-DNA-LHG_250822_L04_exp250213_MS8_SCGE_switch_gDNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2025-09-29-DNA-LHG_250822_L04_exp250213_MS8_SCGE_switch_gDNA.2x36mers.sacCer3 -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py 2025-09-29-DNA-LHG_250822_L04_exp250213_MS8_SCGE_switch_gDNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2025-09-29-DNA-LHG_250822_L04_exp250213_MS8_SCGE_switch_gDNA.2x36mers.sacCer3.nochrM.ERMTOC -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -excludeReadsMappingToOtherChromosomes
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py 2025-09-29-DNA-LHG_250822_L04_exp250213_MS8_SCGE_switch_gDNA.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-2025-09-29-DNA-LHG_250822_L04_exp250213_MS8_SCGE_switch_gDNA.1x36mers.C_glabrata_CBS138_current_chromosomes.unique.nochrM -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py 2025-09-29-DNA-LHG_250822_L04_exp250213_MS8_SCGE_switch_gDNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2025-09-29-DNA-LHG_250822_L04_exp250213_MS8_SCGE_switch_gDNA.2x36mers.C_glabrata_CBS138_current_chromosomes -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py 2025-09-29-DNA-LHG_250822_L04_exp250213_MS8_SCGE_switch_gDNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2025-09-29-DNA-LHG_250822_L04_exp250213_MS8_SCGE_switch_gDNA.2x36mers.C_glabrata_CBS138_current_chromosomes.nochrM.ERMTOC -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -excludeReadsMappingToOtherChromosomes
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py 2025-09-29-DNA-LHG_250822_L05_exp250222_MS8_SCD_gDNA.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-2025-09-29-DNA-LHG_250822_L05_exp250222_MS8_SCD_gDNA.1x36mers.sacCer3.unique.nochrM -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py 2025-09-29-DNA-LHG_250822_L05_exp250222_MS8_SCD_gDNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2025-09-29-DNA-LHG_250822_L05_exp250222_MS8_SCD_gDNA.2x36mers.sacCer3 -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py 2025-09-29-DNA-LHG_250822_L05_exp250222_MS8_SCD_gDNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2025-09-29-DNA-LHG_250822_L05_exp250222_MS8_SCD_gDNA.2x36mers.sacCer3.nochrM.ERMTOC -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -excludeReadsMappingToOtherChromosomes
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py 2025-09-29-DNA-LHG_250822_L05_exp250222_MS8_SCD_gDNA.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-2025-09-29-DNA-LHG_250822_L05_exp250222_MS8_SCD_gDNA.1x36mers.C_glabrata_CBS138_current_chromosomes.unique.nochrM -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py 2025-09-29-DNA-LHG_250822_L05_exp250222_MS8_SCD_gDNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2025-09-29-DNA-LHG_250822_L05_exp250222_MS8_SCD_gDNA.2x36mers.C_glabrata_CBS138_current_chromosomes -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py 2025-09-29-DNA-LHG_250822_L05_exp250222_MS8_SCD_gDNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2025-09-29-DNA-LHG_250822_L05_exp250222_MS8_SCD_gDNA.2x36mers.C_glabrata_CBS138_current_chromosomes.nochrM.ERMTOC -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -excludeReadsMappingToOtherChromosomes
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py 2025-09-29-DNA-LHG_250822_L06_exp250222_MS8_SCGE_gDNA.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-2025-09-29-DNA-LHG_250822_L06_exp250222_MS8_SCGE_gDNA.1x36mers.sacCer3.unique.nochrM -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py 2025-09-29-DNA-LHG_250822_L06_exp250222_MS8_SCGE_gDNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2025-09-29-DNA-LHG_250822_L06_exp250222_MS8_SCGE_gDNA.2x36mers.sacCer3 -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py 2025-09-29-DNA-LHG_250822_L06_exp250222_MS8_SCGE_gDNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2025-09-29-DNA-LHG_250822_L06_exp250222_MS8_SCGE_gDNA.2x36mers.sacCer3.nochrM.ERMTOC -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -excludeReadsMappingToOtherChromosomes
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py 2025-09-29-DNA-LHG_250822_L06_exp250222_MS8_SCGE_gDNA.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-2025-09-29-DNA-LHG_250822_L06_exp250222_MS8_SCGE_gDNA.1x36mers.C_glabrata_CBS138_current_chromosomes.unique.nochrM -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py 2025-09-29-DNA-LHG_250822_L06_exp250222_MS8_SCGE_gDNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2025-09-29-DNA-LHG_250822_L06_exp250222_MS8_SCGE_gDNA.2x36mers.C_glabrata_CBS138_current_chromosomes -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py 2025-09-29-DNA-LHG_250822_L06_exp250222_MS8_SCGE_gDNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2025-09-29-DNA-LHG_250822_L06_exp250222_MS8_SCGE_gDNA.2x36mers.C_glabrata_CBS138_current_chromosomes.nochrM.ERMTOC -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -excludeReadsMappingToOtherChromosomes
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py 2025-09-29-DNA-LHG_250822_L07_exp250222_MS8_SCD_switch_gDNA.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-2025-09-29-DNA-LHG_250822_L07_exp250222_MS8_SCD_switch_gDNA.1x36mers.sacCer3.unique.nochrM -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py 2025-09-29-DNA-LHG_250822_L07_exp250222_MS8_SCD_switch_gDNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2025-09-29-DNA-LHG_250822_L07_exp250222_MS8_SCD_switch_gDNA.2x36mers.sacCer3 -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py 2025-09-29-DNA-LHG_250822_L07_exp250222_MS8_SCD_switch_gDNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2025-09-29-DNA-LHG_250822_L07_exp250222_MS8_SCD_switch_gDNA.2x36mers.sacCer3.nochrM.ERMTOC -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -excludeReadsMappingToOtherChromosomes
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py 2025-09-29-DNA-LHG_250822_L07_exp250222_MS8_SCD_switch_gDNA.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-2025-09-29-DNA-LHG_250822_L07_exp250222_MS8_SCD_switch_gDNA.1x36mers.C_glabrata_CBS138_current_chromosomes.unique.nochrM -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py 2025-09-29-DNA-LHG_250822_L07_exp250222_MS8_SCD_switch_gDNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2025-09-29-DNA-LHG_250822_L07_exp250222_MS8_SCD_switch_gDNA.2x36mers.C_glabrata_CBS138_current_chromosomes -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py 2025-09-29-DNA-LHG_250822_L07_exp250222_MS8_SCD_switch_gDNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2025-09-29-DNA-LHG_250822_L07_exp250222_MS8_SCD_switch_gDNA.2x36mers.C_glabrata_CBS138_current_chromosomes.nochrM.ERMTOC -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -excludeReadsMappingToOtherChromosomes
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py 2025-09-29-DNA-LHG_250822_L08_exp250222_MS8_SCGE_switch_gDNA.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-2025-09-29-DNA-LHG_250822_L08_exp250222_MS8_SCGE_switch_gDNA.1x36mers.sacCer3.unique.nochrM -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py 2025-09-29-DNA-LHG_250822_L08_exp250222_MS8_SCGE_switch_gDNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2025-09-29-DNA-LHG_250822_L08_exp250222_MS8_SCGE_switch_gDNA.2x36mers.sacCer3 -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py 2025-09-29-DNA-LHG_250822_L08_exp250222_MS8_SCGE_switch_gDNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2025-09-29-DNA-LHG_250822_L08_exp250222_MS8_SCGE_switch_gDNA.2x36mers.sacCer3.nochrM.ERMTOC -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -excludeReadsMappingToOtherChromosomes
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py 2025-09-29-DNA-LHG_250822_L08_exp250222_MS8_SCGE_switch_gDNA.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-2025-09-29-DNA-LHG_250822_L08_exp250222_MS8_SCGE_switch_gDNA.1x36mers.C_glabrata_CBS138_current_chromosomes.unique.nochrM -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py 2025-09-29-DNA-LHG_250822_L08_exp250222_MS8_SCGE_switch_gDNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2025-09-29-DNA-LHG_250822_L08_exp250222_MS8_SCGE_switch_gDNA.2x36mers.C_glabrata_CBS138_current_chromosomes -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py 2025-09-29-DNA-LHG_250822_L08_exp250222_MS8_SCGE_switch_gDNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2025-09-29-DNA-LHG_250822_L08_exp250222_MS8_SCGE_switch_gDNA.2x36mers.C_glabrata_CBS138_current_chromosomes.nochrM.ERMTOC -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -excludeReadsMappingToOtherChromosomes
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py 2025-09-29-DNA-LHG_250822_L09_exp250527_MS8_YPD_gDNA.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-2025-09-29-DNA-LHG_250822_L09_exp250527_MS8_YPD_gDNA.1x36mers.sacCer3.unique.nochrM -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py 2025-09-29-DNA-LHG_250822_L09_exp250527_MS8_YPD_gDNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2025-09-29-DNA-LHG_250822_L09_exp250527_MS8_YPD_gDNA.2x36mers.sacCer3 -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py 2025-09-29-DNA-LHG_250822_L09_exp250527_MS8_YPD_gDNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2025-09-29-DNA-LHG_250822_L09_exp250527_MS8_YPD_gDNA.2x36mers.sacCer3.nochrM.ERMTOC -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -excludeReadsMappingToOtherChromosomes
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py 2025-09-29-DNA-LHG_250822_L09_exp250527_MS8_YPD_gDNA.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-2025-09-29-DNA-LHG_250822_L09_exp250527_MS8_YPD_gDNA.1x36mers.C_glabrata_CBS138_current_chromosomes.unique.nochrM -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py 2025-09-29-DNA-LHG_250822_L09_exp250527_MS8_YPD_gDNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2025-09-29-DNA-LHG_250822_L09_exp250527_MS8_YPD_gDNA.2x36mers.C_glabrata_CBS138_current_chromosomes -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py 2025-09-29-DNA-LHG_250822_L09_exp250527_MS8_YPD_gDNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2025-09-29-DNA-LHG_250822_L09_exp250527_MS8_YPD_gDNA.2x36mers.C_glabrata_CBS138_current_chromosomes.nochrM.ERMTOC -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -excludeReadsMappingToOtherChromosomes
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py 2025-09-29-DNA-LHG_250822_L10_exp250527_MS8_SCGE_gDNA.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-2025-09-29-DNA-LHG_250822_L10_exp250527_MS8_SCGE_gDNA.1x36mers.sacCer3.unique.nochrM -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py 2025-09-29-DNA-LHG_250822_L10_exp250527_MS8_SCGE_gDNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2025-09-29-DNA-LHG_250822_L10_exp250527_MS8_SCGE_gDNA.2x36mers.sacCer3 -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py 2025-09-29-DNA-LHG_250822_L10_exp250527_MS8_SCGE_gDNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2025-09-29-DNA-LHG_250822_L10_exp250527_MS8_SCGE_gDNA.2x36mers.sacCer3.nochrM.ERMTOC -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -excludeReadsMappingToOtherChromosomes
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py 2025-09-29-DNA-LHG_250822_L10_exp250527_MS8_SCGE_gDNA.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-2025-09-29-DNA-LHG_250822_L10_exp250527_MS8_SCGE_gDNA.1x36mers.C_glabrata_CBS138_current_chromosomes.unique.nochrM -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py 2025-09-29-DNA-LHG_250822_L10_exp250527_MS8_SCGE_gDNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2025-09-29-DNA-LHG_250822_L10_exp250527_MS8_SCGE_gDNA.2x36mers.C_glabrata_CBS138_current_chromosomes -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py 2025-09-29-DNA-LHG_250822_L10_exp250527_MS8_SCGE_gDNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2025-09-29-DNA-LHG_250822_L10_exp250527_MS8_SCGE_gDNA.2x36mers.C_glabrata_CBS138_current_chromosomes.nochrM.ERMTOC -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -excludeReadsMappingToOtherChromosomes
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py 2025-09-29-DNA-LHG_250822_L11_exp250528_MS8_YPD_gDNA.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-2025-09-29-DNA-LHG_250822_L11_exp250528_MS8_YPD_gDNA.1x36mers.sacCer3.unique.nochrM -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py 2025-09-29-DNA-LHG_250822_L11_exp250528_MS8_YPD_gDNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2025-09-29-DNA-LHG_250822_L11_exp250528_MS8_YPD_gDNA.2x36mers.sacCer3 -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py 2025-09-29-DNA-LHG_250822_L11_exp250528_MS8_YPD_gDNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2025-09-29-DNA-LHG_250822_L11_exp250528_MS8_YPD_gDNA.2x36mers.sacCer3.nochrM.ERMTOC -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -excludeReadsMappingToOtherChromosomes
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py 2025-09-29-DNA-LHG_250822_L11_exp250528_MS8_YPD_gDNA.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-2025-09-29-DNA-LHG_250822_L11_exp250528_MS8_YPD_gDNA.1x36mers.C_glabrata_CBS138_current_chromosomes.unique.nochrM -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py 2025-09-29-DNA-LHG_250822_L11_exp250528_MS8_YPD_gDNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2025-09-29-DNA-LHG_250822_L11_exp250528_MS8_YPD_gDNA.2x36mers.C_glabrata_CBS138_current_chromosomes -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py 2025-09-29-DNA-LHG_250822_L11_exp250528_MS8_YPD_gDNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2025-09-29-DNA-LHG_250822_L11_exp250528_MS8_YPD_gDNA.2x36mers.C_glabrata_CBS138_current_chromosomes.nochrM.ERMTOC -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -excludeReadsMappingToOtherChromosomes
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py 2025-09-29-DNA-LHG_250822_L12_exp250528_MS8_SCGE_gDNA.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-2025-09-29-DNA-LHG_250822_L12_exp250528_MS8_SCGE_gDNA.1x36mers.sacCer3.unique.nochrM -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py 2025-09-29-DNA-LHG_250822_L12_exp250528_MS8_SCGE_gDNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2025-09-29-DNA-LHG_250822_L12_exp250528_MS8_SCGE_gDNA.2x36mers.sacCer3 -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py 2025-09-29-DNA-LHG_250822_L12_exp250528_MS8_SCGE_gDNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2025-09-29-DNA-LHG_250822_L12_exp250528_MS8_SCGE_gDNA.2x36mers.sacCer3.nochrM.ERMTOC -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -excludeReadsMappingToOtherChromosomes
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py 2025-09-29-DNA-LHG_250822_L12_exp250528_MS8_SCGE_gDNA.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-2025-09-29-DNA-LHG_250822_L12_exp250528_MS8_SCGE_gDNA.1x36mers.C_glabrata_CBS138_current_chromosomes.unique.nochrM -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py 2025-09-29-DNA-LHG_250822_L12_exp250528_MS8_SCGE_gDNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2025-09-29-DNA-LHG_250822_L12_exp250528_MS8_SCGE_gDNA.2x36mers.C_glabrata_CBS138_current_chromosomes -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py 2025-09-29-DNA-LHG_250822_L12_exp250528_MS8_SCGE_gDNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2025-09-29-DNA-LHG_250822_L12_exp250528_MS8_SCGE_gDNA.2x36mers.C_glabrata_CBS138_current_chromosomes.nochrM.ERMTOC -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -excludeReadsMappingToOtherChromosomes