Documentation for bam_readcount.cwl

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Overview

bam_readcount workflow

Inputs

Name	Label	Description	Type	Secondary Files
vcf			File	['.tbi']
sample			string
reference_fasta			['string', 'File']	['.fai', '^.dict']
bam			File	['.bai']
min_base_quality			int?
min_mapping_quality			int?

Outputs

Name	Label	Description	Type	Secondary Files
normalized_vcf			File
snv_bam_readcount_tsv			File
indel_bam_readcount_tsv			File

Steps

Name	CWL Run
normalize_variants	tools/normalize_variants.cwl
decompose_variants	tools/vt_decompose.cwl
bam_readcount	tools/bam_readcount.cwl