subworkflows_filter_vcf.cwl

Documentation for filter_vcf.cwl

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Overview

Apply filters to VCF file

Inputs

Name	Label	Description	Type	Secondary Files
vcf			File	['.tbi']
filter_mapq0_threshold			float
filter_gnomADe_maximum_population_allele_frequency			float
gnomad_field_name			string
tumor_bam			File	['.bai']
do_cle_vcf_filter			boolean
filter_somatic_llr_threshold			float
filter_somatic_llr_tumor_purity			float
filter_somatic_llr_normal_contamination_rate			float
filter_minimum_depth			int
tumor_sample_name			string
normal_sample_name			string
validated_variants		An optional VCF with variants that will be flagged as 'VALIDATED' if found in this pipeline's main output VCF	File?	['.tbi']

Outputs

Name	Label	Description	Type	Secondary Files
filtered_vcf			File

Steps

Name	CWL Run
filter_known_variants	tools/filter_known_variants.cwl
filter_vcf_gnomADe_allele_freq	tools/filter_vcf_custom_allele_freq.cwl
filter_vcf_mapq0	tools/filter_vcf_mapq0.cwl
filter_vcf_cle	tools/filter_vcf_cle.cwl
filter_vcf_depth	tools/filter_vcf_depth.cwl
filter_vcf_somatic_llr	tools/filter_vcf_somatic_llr.cwl
set_final_vcf_name	tools/staged_rename.cwl