Description

Filter variants

Input

name:type
description
pattern

meta{:bash}

:map

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

vcf{:bash}

:list

List of VCF(.gz) files

*.{vcf,vcf.gz}

tbi{:bash}

:list

List of VCF file indexes

*.{tbi}

meta2{:bash}

:map

Groovy Map containing reference information e.g. [ id:‘genome’ ]

fasta{:bash}

:file

Fasta file of reference genome

*.fasta

meta3{:bash}

:map

Groovy Map containing reference information e.g. [ id:‘genome’ ]

fai{:bash}

:file

Index of fasta file

*.fasta.fai

meta4{:bash}

:map

Groovy Map containing reference information e.g. [ id:‘genome’ ]

dict{:bash}

:file

Sequence dictionary of fastea file

*.dict

meta5{:bash}

:map

Groovy Map containing reference information e.g. [ id:‘genome’ ]

gzi{:bash}

:file

Genome index file only needed when the genome file was compressed with the BGZF algorithm.

*.gzi

Output

name:type
description
pattern

vcf{:bash}

meta{:bash}

:file

Compressed VCF file

*.vcf.gz

*.vcf.gz{:bash}

:file

Compressed VCF file

*.vcf.gz

tbi{:bash}

meta{:bash}

:file

Compressed VCF file

*.vcf.gz

*.tbi{:bash}

:file

Index of VCF 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/categories/360002369672s 10.1158/1538-7445.AM2017-3590
included in
genomicrelatednesspathogensurveillancerarediseasernadnavarrnavarvariantcatalogue
maintainers
Github user kevinmenden
Github user ramprasadn
get in touch
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