Nextflow Registry | nf-core/plink2/vcf2bgen@0.0.0-0c7146d

nf-core/plink2/vcf2bgen @ 0.0.0-0c7146d

Convert from VCF file to BGEN file version 1.2 format preserving dosages.

plink2 bgen file vcf file genotype dosages

Latest version: 0.0.0-0c7146d

Total downloads: 1

Source: nf-core/modules

Authors: @edg1983

Maintainers: @edg1983

Convert from VCF file to BGEN file version 1.2 format preserving dosages.

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

include { PLINK2_VCF2BGEN } from 'nf-core/plink2/vcf2bgen'

MIT License

Process

`Name`	`PLINK2_VCF2BGEN`

Input 1 channel

#1 tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1', single_end:false ]`
`vcf` file	A vcf or vcf.gz file with genetic variants `*.{vcf,vcf.gz}`
`dosage_field` string	The FORMAT field that contains the dosage information. Set to DS to when a dosage field is not present.
`bgen_reffirst` boolean	Set true to write BGEN file with ref-first flag. With this option the first allele in the BGEN correspond to the REF allele.
`sample_name_mode` string	Option to use to set IID/FID in the BGEN file. Allowed values are double-id, const-fid , or id-delim .

Output 4 channels

#1 log_file tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1', single_end:false ]`
`*.log` file	Log file generated by plink2 with information on the process applied `*.log`

#2 versions

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

#3 bgen_file tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1', single_end:false ]`
`*.bgen` file	BGEN file version 1.2 `*.bgen`

#4 sample_file tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1', single_end:false ]`
`*.sample` file	Sample file defining samples in the BGEN `*.sample`

Tool	Description	Homepage
plink2	Whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner	http://www.cog-genomics.org/plink/2.0/

Version	0.0.0-0c7146d
Commit ID	135d883a43b1a2324b4112cd270cf22e20835533
Release Date	08 Apr 2026 19:04:40 (UTC)
Download URL	https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Fplink2%2Fvcf2bgen/0.0.0-0c7146d/download
OCI Store URL	https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/plink2/vcf2bgen/blobs/sha256:1279b8bb80912e550a474cd316ea5d8de706f23ecf8d02eb860651e686df60c0
Size	3.1 KB
Checksum	sha256:1279b8bb80912e550a474cd316ea5d8de706f23ecf8d02eb860651e686df60c0
Downloads	1

Version	Date	Status	Downloads	Size	Diff
0.0.0-0c7146d	08 Apr 2026 19:04:40 (UTC)		1	3.1 KB	-