A list of common argument names

arguments

• tumor_bam tumor bam file

• normal_bam normal bam file

• tumor_sample tumor samplename

• normal_sample normal reference

• out_prefix a combination of tumor and normal name used as out-prefix in several commands

• fqs_tum_1

• fqs_tum_2

• fqs_ref_1

• fqs_ref_2

function names

• preprocess
• mutect
• bwa
• samtools_sort
• samtools_merge
• samtools_index

pipeline names

• bam_preprocess
• bam_mutect: take two bams, preprocess and perform mutect