modules/gatk_realignertargetcreator

Generates a list of locations that should be considered for local realignment prior genotyping.

bamvcfvariant callingindelrealignmenttargets

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

Description

Generates a list of locations that should be considered for local realignment prior genotyping.

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/CRAM/SAM file

*.bam

`bai:file`

BAM index file

*.bai

`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

`intervals`

`meta:map`

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

`*.intervals:file`

File containing intervals that represent sites of extant and potential indels.

*.intervals

`s:file`

File containing intervals that represent sites of extant and potential indels.

*.intervals

`versions`

`versions.yml:file`

File containing software versions

versions.yml

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_realignertargetcreator

Description

Input

meta:map

bam:file

bai:file

meta2:map

fasta:file

meta3:map

fai:file

meta4:map

dict:file

meta5:map

known_vcf:file

Output

intervals

meta:map

*.intervals:file

s:file

versions

versions.yml:file

Tools

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

`meta:map`

`bam:file`

`bai:file`

`meta2:map`

`fasta:file`

`meta3:map`

`fai:file`

`meta4:map`

`dict:file`

`meta5:map`

`known_vcf:file`

`intervals`

`meta:map`

`*.intervals:file`

`s:file`

`versions`

`versions.yml:file`

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