modules/gatk4_mergevcfs

Merges several vcf files

gatk4mergevcf

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

Description

Merges several vcf files

Input

name:type

description

pattern

`meta:map`

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

`vcf:list`

Two or more VCF files

*.{vcf,vcf.gz}

`meta2:map`

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

`dict:file`

Optional Sequence Dictionary as input

*.dict

Output

name:type

description

pattern

`vcf`

`meta:file`

merged vcf file

*.vcf.gz

`*.vcf.gz:file`

merged vcf file

*.vcf.gz

`tbi`

`meta:file`

index files for the merged vcf files

*.tbi

`*.tbi:file`

index files for the merged vcf files

*.tbi

`versions`

`versions.yml:file`

File containing software versions

versions.yml

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

modules/gatk4_mergevcfs

Description

Input

`meta:map`

`vcf:list`

`meta2:map`

`dict:file`

Output

`vcf`

`meta:file`

`*.vcf.gz:file`

`tbi`

`meta:file`

`*.tbi:file`

`versions`

`versions.yml:file`

Tools

gatk4
Apache-2.0

included in

maintainer

get in touch

modules/gatk4_mergevcfs

Description

Input

meta:map

vcf:list

meta2:map

dict:file

Output

vcf

meta:file

*.vcf.gz:file

tbi

meta:file

*.tbi:file

versions

versions.yml:file

Tools

gatk4 Apache-2.0

included in

maintainer

get in touch

`meta:map`

`vcf:list`

`meta2:map`

`dict:file`

`vcf`

`meta:file`

`*.vcf.gz:file`

`tbi`

`meta:file`

`*.tbi:file`

`versions`

`versions.yml:file`

gatk4
Apache-2.0