Nextflow Registry | nf-core/vt/normalize@0.0.0-6c4ed3a

nf-core/vt/normalize @ 0.0.0-6c4ed3a

normalizes variants in a VCF file

normalization vcf snps indels

Latest version: 0.0.0-6c4ed3a

Total downloads: 11

Source: nf-core/modules

Authors: @nvnieuwk

Maintainers: @nvnieuwk

normalizes variants in a VCF file

Add the following snippet to your workflow script to include this module.

include { VT_NORMALIZE } from 'nf-core/vt/normalize'

MIT License

Process

`Name`	`VT_NORMALIZE`

Input 3 channels

#1 tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'test', single_end:false ]`
`vcf` file	The VCF file to normalize `*.vcf(.gz)?`
`tbi` file	The tabix index of the VCF file when bgzipped `*.tbi`
`intervals` file	The intervals of the variants of normalize `*.bed`

#2 tuple

`meta2` map	Groovy Map containing reference information e.g. `[ id:'test', single_end:false ]`
`fasta` file	The reference fasta file `*.{fasta,fn,fna,fa}`

#3 tuple

`meta3` map	Groovy Map containing reference index information e.g. `[ id:'test', single_end:false ]`
`fai` file	The index of the reference fasta file (OPTIONAL) `*.fai`

Output 3 channels

#1 fai tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'test', single_end:false ]`
`${fasta}.fai` file	The created index of the reference fasta file (only when the fai wasn't supplied) `*.fai`

#2 vcf tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'test', single_end:false ]`
`*.vcf.gz` file	The normalized VCF file `*.vcf.gz`

#3 versions

`versions.yml` file	File containing software versions `versions.yml`

Tool	Description	Homepage
vt	A tool set for short variant discovery in genetic sequence data	https://genome.sph.umich.edu/wiki/Vt

Version	0.0.0-6c4ed3a
Commit ID	6c4ed3a220310b905a1fc9d04f05be2e0837142b
Release Date	23 Apr 2026 15:52:52 (UTC)
Download URL	https://registry.nextflow.io/api/v1/modules/nf-core%2Fvt%2Fnormalize/0.0.0-6c4ed3a/download
OCI Store URL	https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/vt/normalize/blobs/sha256:e215b2640a84ef7efe9e3aa671b8aa06ead1520c9ca1950abc54eeab23b73ac1
Size	3.1 KB
Checksum	sha256:e215b2640a84ef7efe9e3aa671b8aa06ead1520c9ca1950abc54eeab23b73ac1
Downloads	4

Version	Date	Downloads	Size
0.0.0-6c4ed3a	23 Apr 2026 15:52:52 (UTC)	4	3.1 KB
0.0.0-3fc6d40	22 Apr 2026 15:36:46 (UTC)	3	3.1 KB
0.0.0-0c7146d	08 Apr 2026 19:47:28 (UTC)	4	3.1 KB