Description

Apply tranche filtering

Input

name:type
description
pattern

meta:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end

]

vcf:file

a VCF file containing variants, must have info key

*.vcf.gz

tbi:file

tbi file matching with -vcf

*.vcf.gz.tbi

intervals:file

Intervals

resources:list

resource A VCF containing known SNP and or INDEL sites. Can be supplied as many times as necessary

*.vcf.gz

resources_index:list

Index of resource VCF containing known SNP and or INDEL sites. Can be supplied as many times as necessary

*.vcf.gz

fasta:file

The reference fasta file

*.fasta

fai:file

Index of reference fasta file

fasta.fai

dict:file

GATK sequence dictionary

.dict

Output

name:type
description
pattern

vcf

meta:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end

]

*.vcf.gz:file

VCF file

*.vcf.gz

tbi

meta:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end

]

*.vcf.gz.tbi:file

VCF index file

*.vcf.gz.tbi

versions

versions.yml:file

File containing software versions

versions.yml

Tools

gatk4
Apache-2.0

Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size.

gatk.broadinstitute.org/hc/en-us gatk.broadinstitute.org/hc/en-us/articles/360051308071-FilterVariantTranches 10.1158/1538-7445.AM2017-3590
included in
sarek
maintainer
Github user FriederikeHanssen
get in touch
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