Description

Perform joint genotyping on one or more samples pre-called with HaplotypeCaller.

Input

name:type
description
pattern

meta{:bash}

:map

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

input{:bash}

:file

gVCF(.gz) file or a GenomicsDB

*.{vcf,vcf.gz}

gvcf_index{:bash}

:file

index of gvcf file, or empty when providing GenomicsDB

*.{idx,tbi}

intervals{:bash}

:file

Interval file with the genomic regions included in the library (optional)

intervals_index{:bash}

:file

Interval index file (optional)

meta2{:bash}

:map

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

fasta{:bash}

:file

Reference fasta file

*.fasta

meta3{:bash}

:map

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

fai{:bash}

:file

Reference fasta index file

*.fai

meta4{:bash}

:map

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

dict{:bash}

:file

Reference fasta sequence dict file

*.dict

meta5{:bash}

:map

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

dbsnp{:bash}

:file

dbSNP VCF file

*.vcf.gz

meta6{:bash}

:map

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

dbsnp_tbi{:bash}

:file

dbSNP VCF index file

*.tbi

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

Genotyped VCF file

*.vcf.gz

tbi{:bash}

meta{:bash}

:map

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

*.tbi{:bash}

:file

Tbi index for VCF file

*.vcf.gz

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

included in
genomicrelatednesssarek
maintainers
Github user santiagorevale
Github user maxulysse
get in touch
Ask a question on Slack Open an issue on GitHub