modules/gatk_indelrealigner

Performs local realignment around indels to correct for mapping errors

bamvcfvariant callingindelrealignment

https://github.com/nf-core/modules/[...]/modules/nf-core/gatk/indelrealigner

Description

Performs local realignment around indels to correct for mapping errors

Input

name:type

description

pattern

`meta`
`:map`

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

`bam`
`:file`

Sorted and indexed BAM file

*.bam

`bai`
`:file`

BAM index file

*.bai

`intervals`
`:file`

Intervals file created by gatk3 RealignerTargetCreator

*.{intervals,list}

`meta2`
`:map`

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

`fasta`
`:file`

Reference file used to generate BAM file

.{fasta,fa,fna}

`meta3`
`:map`

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

`fai`
`:file`

Index of reference file used to generate BAM file

.fai

`meta4`
`:map`

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

`dict`
`:file`

GATK dict file for reference

.dict

`meta5`
`:map`

Groovy Map containing file meta-information for known_vcf. e.g. [ id:‘test’, single_end:false ]

`known_vcf`
`:file`

Optional input VCF file(s) with known indels

.vcf

Output

name:type

description

pattern

`bam`

`meta`
`:map`

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

`*.bam`
`:file`

Sorted and indexed BAM file with local realignment around variants

*.bam

`*.bai`
`:file`

Sorted and indexed BAM file with local realignment around variants

*.bam

`versions_gatk`

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

The name of the process

`gatk`
`:string`

The name of the tool

`gatk3 --version`
`:eval`

The expression to obtain the version of the tool

Topics

name:type

description

pattern

`versions`

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

The name of the process

`gatk`
`:string`

The name of the tool

`gatk3 --version`
`:eval`

The expression to obtain the version of the tool

Tools

gatk
https://software.broadinstitute.org/gatk/download/licensing BSD https://www.broadinstitute.org/gatk/about/#licensing

The full Genome Analysis Toolkit (GATK) framework, license restricted.

gatk.broadinstitute.org/hc/en-us github.com/broadinstitute/gatk-docs

modules/gatk_indelrealigner

Description

Input

`meta`
`:map`

`bam`
`:file`

`bai`
`:file`

`intervals`
`:file`

`meta2`
`:map`

`fasta`
`:file`

`meta3`
`:map`

`fai`
`:file`

`meta4`
`:map`

`dict`
`:file`

`meta5`
`:map`

`known_vcf`
`:file`

Output

`bam`

`meta`
`:map`

`*.bam`
`:file`

`*.bai`
`:file`

`versions_gatk`

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

`gatk`
`:string`

`gatk3 --version`
`:eval`

Topics

`versions`

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

`gatk`
`:string`

`gatk3 --version`
`:eval`

Tools

gatk
https://software.broadinstitute.org/gatk/download/licensing BSD https://www.broadinstitute.org/gatk/about/#licensing

maintainer

get in touch

modules/gatk_indelrealigner

Description

Input

meta:map

bam:file

bai:file

intervals:file

meta2:map

fasta:file

meta3:map

fai:file

meta4:map

dict:file

meta5:map

known_vcf:file

Output

bam

meta:map

*.bam:file

*.bai:file

versions_gatk

${task.process}:string

gatk:string

gatk3 --version:eval

Topics

versions

${task.process}:string

gatk:string

gatk3 --version:eval

Tools

gatk https://software.broadinstitute.org/gatk/download/licensing BSD https://www.broadinstitute.org/gatk/about/#licensing

maintainer

get in touch

`meta`
`:map`

`bam`
`:file`

`bai`
`:file`

`intervals`
`:file`

`meta2`
`:map`

`fasta`
`:file`

`meta3`
`:map`

`fai`
`:file`

`meta4`
`:map`

`dict`
`:file`

`meta5`
`:map`

`known_vcf`
`:file`

`bam`

`meta`
`:map`

`*.bam`
`:file`

`*.bai`
`:file`

`versions_gatk`

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

`gatk`
`:string`

`gatk3 --version`
`:eval`

`versions`

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

`gatk`
`:string`

`gatk3 --version`
`:eval`

gatk
https://software.broadinstitute.org/gatk/download/licensing BSD https://www.broadinstitute.org/gatk/about/#licensing