Documentation for varscan_germline.cwl

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Overview

Varscan Workflow

Inputs

Name	Label	Description	Type	Secondary Files
reference			['string', 'File']	['.fai', '^.dict']
bam			File	['.bai', '^.bai']
interval_list			File
strand_filter			int?
min_coverage			int?
min_var_freq			float?
min_reads			int?
p_value			float?
max_normal_freq			float?
sample_name			string

Outputs

Name	Label	Description	Type	Secondary Files
unfiltered_vcf			File	['.tbi']
filtered_vcf			File	['.tbi']

Steps

Name	CWL Run
intervals_to_bed	tools/intervals_to_bed.cwl
varscan	tools/varscan_germline.cwl
bgzip_and_index	subworkflows/bgzip_and_index.cwl
filter	subworkflows/fp_filter.cwl