Nextflow Registry | nf-core/bcftools/merge@0.0.0-0c7146d

nf-core/bcftools/merge @ 0.0.0-0c7146d

Merge VCF files

variant calling merge VCF

Latest version: 0.0.0-0c7146d

Total downloads: 1

Source: nf-core/modules

Authors: @joseespinosa @drpatelh @nvnieuwk @ramprasadn

Maintainers: @joseespinosa @drpatelh @nvnieuwk @ramprasadn

Merge VCF files

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

include { BCFTOOLS_MERGE } from 'nf-core/bcftools/merge'

MIT License

Process

`Name`	`BCFTOOLS_MERGE`

Input 2 channels

#1 tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`vcfs` file	List containing 2 or more vcf files e.g. [ 'file1.vcf', 'file2.vcf' ]
`tbis` file	List containing the tbi index files corresponding to the vcfs input files e.g. [ 'file1.vcf.tbi', 'file2.vcf.tbi' ]
`bed` file	(Optional) The bed regions to merge on `*.bed`

#2 tuple

`meta2` map	Groovy Map containing reference information e.g. [ id:'genome' ]
`fasta` file	(Optional) The fasta reference file (only necessary for the `--gvcf FILE` parameter) `*.{fasta,fa}`
`fai` file	(Optional) The fasta reference file index (only necessary for the `--gvcf FILE` parameter) `*.fai`

Output 3 channels

#1 vcf tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.{bcf,vcf}{,.gz}` file	merged output file `*.{vcf,vcf.gz,bcf,bcf.gz}`

#2 index tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.{csi,tbi}` file	index of merged output `*.{csi,tbi}`

#3 versions_bcftools tuple

`${task.process}` string	The process the versions were collected from
`bcftools` string	The tool name
`bcftools --version \| sed '1!d; s/^.*bcftools //'` string	The command used to generate the version of the tool

Tool	Description	Homepage
merge	Merge VCF files.	http://samtools.github.io/bcftools/bcftools.html

Version	0.0.0-0c7146d
Commit ID	135d883a43b1a2324b4112cd270cf22e20835533
Release Date	08 Apr 2026 18:25:15 (UTC)
Download URL	https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Fbcftools%2Fmerge/0.0.0-0c7146d/download
OCI Store URL	https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/bcftools/merge/blobs/sha256:3d45827e83c374b8d38be3f52ee478f8735d028392d6782a22c4b35814e4f04c
Size	4.3 KB
Checksum	sha256:3d45827e83c374b8d38be3f52ee478f8735d028392d6782a22c4b35814e4f04c
Downloads	1

Version	Date	Status	Downloads	Size	Diff
0.0.0-0c7146d	08 Apr 2026 18:25:15 (UTC)		1	4.3 KB	-