Description

Select a subset of variants from a VCF file

Input

name:type
description
pattern

meta{:bash}

:map

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

vcf{:bash}

:list

VCF(.gz) file

*.{vcf,vcf.gz}

vcf_idx{:bash}

:list

VCF file index

*.{idx,tbi}

intervals{:bash}

:file

One or more genomic intervals over which to operate

.intervals

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

Compressed VCF file

*.selectvariants.vcf.gz

tbi{:bash}

meta{:bash}

:map

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

*.vcf.gz.tbi{:bash}

:file

Tabix index file

*.vcf.gz.tbi

versions_gatk4{:bash}

${task.process}{:bash}

:string

The name of the process

gatk4{:bash}

:string

The name of the tool

gatk --version | sed -n '/GATK.*v/s/.*v//p'{:bash}

:eval

The expression to obtain the version of the tool

Topics

name:type
description
pattern

versions{:bash}

${task.process}{:bash}

:string

The name of the process

gatk4{:bash}

:string

The name of the tool

gatk --version | sed -n '/GATK.*v/s/.*v//p'{:bash}

:eval

The expression to obtain the version of the tool

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/360036362532-SelectVariants https://github.com/broadinstitute/gatk 10.1158/1538-7445.AM2017-3590
included in
genomicrelatednessrarediseasetbanalyzer
maintainers
Github user mjcipriano
Github user ramprasadn
get in touch
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