Workflow: genotype and filter subworkflow

Fetched 2020-03-30 18:15:54 GMT

Perform genotyping and filtration over a given genomic interval. Takes one or more GVCFs (from HaplotypeCaller) as input.

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Inputs

ID Type Title Doc
dbsnp File (Optional)
variant File[]
ref_fasta File
interval File (Optional)

Steps

ID Runs Label Doc
gatk_combine_gvcfs
../tools/gatk-CombineGVCFs.cwl (CommandLineTool)
GATK CombineGVCFs

Merges one or more HaplotypeCaller GVCF files into a single GVCF with appropriate annotations. This tool was created to run as part of the \"haplotype_caller\" workflow. Some parameters may be used differently than they are in the standalone program. Tool configured to run with version 4.0.10.0 of gatk, available here: https://github.com/broadinstitute/gatk/releases/tag/4.0.10.0

gatk_make_sites_only_vcf
../tools/gatk-MakeSitesOnlyVcf.cwl (CommandLineTool)
GATK MakeSitesOnlyVcf

Creates a VCF that contains all the site-level information for all records in the input VCF but no genotype information. This tool was created to run as part of the \"haplotype_caller\" workflow. Some parameters may be used differently than they are in the standalone program. Tool configured to run with version 4.0.10.0 of gatk, available here: https://github.com/broadinstitute/gatk/releases/tag/4.0.10.0

gatk_variant_filtration
../tools/gatk-VariantFiltration.cwl (CommandLineTool)
GATK VariantFiltration

Filter variant calls based on INFO and/or FORMAT annotations. This tool was created to run as part of the \"haplotype_caller\" workflow. Some parameters may be used differently than they are in the standalone program. Tool configured to run with version 4.0.10.0 of gatk, available here: https://github.com/broadinstitute/gatk/releases/tag/4.0.10.0

gatk_genotype_gvcfs
../tools/gatk-GenotypeGVCFs.cwl (CommandLineTool)
GATK GenotypeGVCFs

Perform joint genotyping on one or more samples pre-called with HaplotypeCaller. This tool was created to run as part of the \"haplotype_caller\" workflow. Some parameters may be used differently than they are in the standalone program. Tool configured to run with version 4.0.10.0 of gatk, available here: https://github.com/broadinstitute/gatk/releases/tag/4.0.10.0

Outputs

ID Type Label Doc
sites_vcf File
filtered_vcf File
Permalink: https://w3id.org/cwl/view/git/eed6e100a29e8a1faa8ad6da62c4490ee2a88db9/workflows/genotype_and_filter_subworkflow.cwl