modules/vcflib_vcffixup

Generates a VCF stream where AC and NS have been generated for each record using sample genotypes.

vcfvcflibvcflib/vcffixupAC/NS/AF

https://github.com/nf-core/modules/[...]/modules/nf-core/vcflib/vcffixup

Description

Generates a VCF stream where AC and NS have been generated for each record using sample genotypes.

Input

name:type

description

pattern

`meta:map`

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

]

`vcf:file`

Compressed VCF file

*.{.vcf.gz,vcf}

`tbi:file`

Index of VCF file

*.vcf.gz.tbi

Output

name:type

description

pattern

`vcf`

`meta:map`

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

]

`*.vcf.gz:file`

Compressed VCF file

*.vcf.gz

`versions`

`versions.yml:file`

File containing software versions

versions.yml

Tools

vcflib
MIT

Command-line tools for manipulating VCF files

github.com/vcflib/vcflib github.com/vcflib/vcflib#USAGE 10.1101/2021.05.21.445151

modules/vcflib_vcffixup

Description

Input

`meta:map`

`vcf:file`

`tbi:file`

Output

`vcf`

`meta:map`

`*.vcf.gz:file`

`versions`

`versions.yml:file`

Tools

vcflib
MIT

included in

maintainer

get in touch

modules/vcflib_vcffixup

Description

Input

meta:map

vcf:file

tbi:file

Output

vcf

meta:map

*.vcf.gz:file

versions

versions.yml:file

Tools

vcflib MIT

included in

maintainer

get in touch

`meta:map`

`vcf:file`

`tbi:file`

`vcf`

`meta:map`

`*.vcf.gz:file`

`versions`

`versions.yml:file`

vcflib
MIT