Description

Apply tranche filtering

Input

name:type
description
pattern

meta{:bash}

:map

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

vcf{:bash}

:file

a VCF file containing variants, must have info key:CNN_2D

*.vcf.gz

tbi{:bash}

:file

tbi file matching with -vcf

*.vcf.gz.tbi

intervals{:bash}

:file

Intervals

resources{:bash}

:list

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

*.vcf.gz

resources_index{:bash}

:list

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

*.vcf.gz

fasta{:bash}

:file

The reference fasta file

*.fasta

fai{:bash}

:file

Index of reference fasta file

fasta.fai

dict{:bash}

:file

GATK sequence dictionary

.dict

Output

name:type
description
pattern

vcf{:bash}

meta{:bash}

:map

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

*.vcf.gz{:bash}

:file

VCF file

*.vcf.gz

tbi{:bash}

meta{:bash}

:map

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

*.vcf.gz.tbi{:bash}

:file

VCF index file

*.vcf.gz.tbi

versions{:bash}

versions.yml{:bash}

: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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