modules/gvcftools_extractvariants

Removes all non-variant blocks from a gVCF file to produce a smaller variant-only VCF file.

gvcftoolsextract_variantsextractvariantsgvcfvcf

https://github.com/nf-core/modules/[...]/modules/nf-core/gvcftools/extractvariants

Description

Removes all non-variant blocks from a gVCF file to produce a smaller variant-only VCF file.

Input

Name (Type)

Description

Pattern

`meta` (map)

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

]

`gvcf` (file)

GVCF file

*.{g.vcf,gvcf}.gz

Output

Name (Type)

Description

Pattern

`meta` (map)

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

]

`versions` (file)

File containing software versions

versions.yml

`vcf` (file)

Converted variant-only VCF file

*.vcf.gz

Tools

gvcftools
MIT

gvcftools is a package of small utilities for creating and analyzing gVCF files

sites.google.com/site/gvcftools/home sites.google.com/site/gvcftools/home/configuration-and-analysis https://github.com/sequencing/gvcftools

modules/gvcftools_extractvariants

Description

Input

`meta` (map)

`gvcf` (file)

Output

`meta` (map)

`versions` (file)

`vcf` (file)

maintainer

get in touch

Tools

gvcftools
MIT

modules/gvcftools_extractvariants

Description

Input

meta (map)

gvcf (file)

Output

meta (map)

versions (file)

vcf (file)

maintainer

get in touch

Tools

gvcftools MIT

`meta` (map)

`gvcf` (file)

`meta` (map)

`versions` (file)

`vcf` (file)

gvcftools
MIT