Documentation for docm_germline.cwl

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Overview

Detect DoCM variants

Inputs

Name	Label	Description	Type	Secondary Files
reference			['string', 'File']	['.fai', '^.dict']
bam			File	['^.bai']
docm_vcf			File	['.tbi']
interval_list			File

Outputs

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

Steps

Name	CWL Run
gatk_haplotypecaller	tools/docm_gatk_haplotype_caller.cwl
bgzip	tools/bgzip.cwl
index	tools/index_vcf.cwl
decompose	tools/vt_decompose.cwl
docm_filter	tools/single_sample_docm_filter.cwl
bgzip2	tools/bgzip.cwl
index2	tools/index_vcf.cwl