modules/gatk4_genotypegvcfs

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

gatk4genotypegvcfjoint genotyping

https://github.com/nf-core/modules/[...]/modules/nf-core/gatk4/genotypegvcfs

Description

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

Input

name:type

description

pattern

`meta`
`:map`

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

`input`
`:file`

gVCF(.gz) file or a GenomicsDB

*.{vcf,vcf.gz}

`gvcf_index`
`:file`

index of gvcf file, or empty when providing GenomicsDB

*.{idx,tbi}

`intervals`
`:file`

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

`intervals_index`
`:file`

Interval index file (optional)

`meta2`
`:map`

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

`fasta`
`:file`

Reference fasta file

*.fasta

`meta3`
`:map`

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

`fai`
`:file`

Reference fasta index file

*.fai

`meta4`
`:map`

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

`dict`
`:file`

Reference fasta sequence dict file

*.dict

`meta5`
`:map`

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

`dbsnp`
`:file`

dbSNP VCF file

*.vcf.gz

`meta6`
`:map`

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

`dbsnp_tbi`
`:file`

dbSNP VCF index file

*.tbi

Output

name:type

description

pattern

`vcf`

`meta`
`:map`

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

`*.vcf.gz`
`:file`

Genotyped VCF file

*.vcf.gz

`tbi`

`meta`
`:map`

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

`*.tbi`
`:file`

Tbi index for VCF file

*.vcf.gz

`versions_gatk4`

`${task.process}`
`:string`

The name of the process

`gatk4`
`:string`

The name of the tool

`gatk --version | sed -n '/GATK.v/s/.v//p'`
`:eval`

The expression to obtain the version of the tool

Topics

name:type

description

pattern

`versions`

`${task.process}`
`:string`

The name of the process

`gatk4`
`:string`

The name of the tool

`gatk --version | sed -n '/GATK.v/s/.v//p'`
`:eval`

The expression to obtain the version of the tool

Tools

gatk4
BSD-3-clause

Genome Analysis Toolkit (GATK4)

gatk.broadinstitute.org/hc/en-us gatk.broadinstitute.org/hc/en-us/categories/360002369672s https://github.com/broadinstitute/gatk 10.1158/1538-7445.AM2017-3590

modules/gatk4_genotypegvcfs

Description

Input

`meta`
`:map`

`input`
`:file`

`gvcf_index`
`:file`

`intervals`
`:file`

`intervals_index`
`:file`

`meta2`
`:map`

`fasta`
`:file`

`meta3`
`:map`

`fai`
`:file`

`meta4`
`:map`

`dict`
`:file`

`meta5`
`:map`

`dbsnp`
`:file`

`meta6`
`:map`

`dbsnp_tbi`
`:file`

Output

`vcf`

`meta`
`:map`

`*.vcf.gz`
`:file`

`tbi`

`meta`
`:map`

`*.tbi`
`:file`

`versions_gatk4`

`${task.process}`
`:string`

`gatk4`
`:string`

`gatk --version | sed -n '/GATK.v/s/.v//p'`
`:eval`

Topics

`versions`

`${task.process}`
`:string`

`gatk4`
`:string`

`gatk --version | sed -n '/GATK.v/s/.v//p'`
`:eval`

Tools

gatk4
BSD-3-clause

included in

maintainers

get in touch

modules/gatk4_genotypegvcfs

Description

Input

meta:map

input:file

gvcf_index:file

intervals:file

intervals_index:file

meta2:map

fasta:file

meta3:map

fai:file

meta4:map

dict:file

meta5:map

dbsnp:file

meta6:map

dbsnp_tbi:file

Output

vcf

meta:map

*.vcf.gz:file

tbi

meta:map

*.tbi:file

versions_gatk4

${task.process}:string

gatk4:string

gatk --version | sed -n '/GATK.*v/s/.*v//p':eval

Topics

versions

${task.process}:string

gatk4:string

gatk --version | sed -n '/GATK.*v/s/.*v//p':eval

Tools

gatk4 BSD-3-clause

included in

maintainers

get in touch

`meta`
`:map`

`input`
`:file`

`gvcf_index`
`:file`

`intervals`
`:file`

`intervals_index`
`:file`

`meta2`
`:map`

`fasta`
`:file`

`meta3`
`:map`

`fai`
`:file`

`meta4`
`:map`

`dict`
`:file`

`meta5`
`:map`

`dbsnp`
`:file`

`meta6`
`:map`

`dbsnp_tbi`
`:file`

`vcf`

`meta`
`:map`

`*.vcf.gz`
`:file`

`tbi`

`meta`
`:map`

`*.tbi`
`:file`

`versions_gatk4`

`${task.process}`
`:string`

`gatk4`
`:string`

`gatk --version | sed -n '/GATK.v/s/.v//p'`
`:eval`

`versions`

`${task.process}`
`:string`

`gatk4`
`:string`

`gatk --version | sed -n '/GATK.v/s/.v//p'`
`:eval`

gatk4
BSD-3-clause