python /oak/stanford/groups/akundaje/marinovg/programs/bwa-meth/bwameth.py --threads 16 --reference ~/Stanford_bootcamp/combined_indexes/bismarck_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa L289-30fL_B_dSMF.end1.75mers_val_1.fq.gz L289-30fL_B_dSMF.end2.75mers_val_2.fq.gz | ~/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT ~/Stanford_bootcamp/combined_indexes/bismarck_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa - | ~/programs/samtools-0.1.18/samtools sort - L289-30fL_B_dSMF.bwameth.sacCer3+C_glabrata_CBS138_current_chromosomes
python /oak/stanford/groups/akundaje/marinovg/programs/bwa-meth/bwameth.py --threads 16 --reference ~/Stanford_bootcamp/combined_indexes/bismarck_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa L290-30fL_A_dSMF.end1.75mers_val_1.fq.gz L290-30fL_A_dSMF.end2.75mers_val_2.fq.gz | ~/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT ~/Stanford_bootcamp/combined_indexes/bismarck_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa - | ~/programs/samtools-0.1.18/samtools sort - L290-30fL_A_dSMF.bwameth.sacCer3+C_glabrata_CBS138_current_chromosomes
python /oak/stanford/groups/akundaje/marinovg/programs/bwa-meth/bwameth.py --threads 16 --reference ~/Stanford_bootcamp/combined_indexes/bismarck_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa L291-60fL_D_dSMF.end1.75mers_val_1.fq.gz L291-60fL_D_dSMF.end2.75mers_val_2.fq.gz | ~/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT ~/Stanford_bootcamp/combined_indexes/bismarck_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa - | ~/programs/samtools-0.1.18/samtools sort - L291-60fL_D_dSMF.bwameth.sacCer3+C_glabrata_CBS138_current_chromosomes
python /oak/stanford/groups/akundaje/marinovg/programs/bwa-meth/bwameth.py --threads 16 --reference ~/Stanford_bootcamp/combined_indexes/bismarck_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa L292-90fL_E_dSMF.end1.75mers_val_1.fq.gz L292-90fL_E_dSMF.end2.75mers_val_2.fq.gz | ~/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT ~/Stanford_bootcamp/combined_indexes/bismarck_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa - | ~/programs/samtools-0.1.18/samtools sort - L292-90fL_E_dSMF.bwameth.sacCer3+C_glabrata_CBS138_current_chromosomes
python /oak/stanford/groups/akundaje/marinovg/programs/bwa-meth/bwameth.py --threads 16 --reference ~/Stanford_bootcamp/combined_indexes/bismarck_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa L293-90fL_F_dSMF.end1.75mers_val_1.fq.gz L293-90fL_F_dSMF.end2.75mers_val_2.fq.gz | ~/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT ~/Stanford_bootcamp/combined_indexes/bismarck_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa - | ~/programs/samtools-0.1.18/samtools sort - L293-90fL_F_dSMF.bwameth.sacCer3+C_glabrata_CBS138_current_chromosomes