Nextflow Registry | nf-core/varscan/processsomatic@0.0.0-0c7146d

nf-core/varscan/processsomatic @ 0.0.0-0c7146d

VarScan2 is a tool for variant detection in massively parallel sequencing data. It can detect SNPs, indels, and copy number variations in both somatic and germline samples. It is particularly useful for analyzing tumor/normal sample pairs. This subtool divides variants based on status (germline, somatic, loss of heterozygosity) and confidence level (high-confidence or not) and outputs them in separate VCF files.

variant calling germline somatic vcf variants genomics

Latest version: 0.0.0-0c7146d

Total downloads: 1

Source: nf-core/modules

Authors: @vmelichar

Maintainers: @vmelichar

Summary

Get started

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

include { VARSCAN_PROCESSSOMATIC } from 'nf-core/varscan/processsomatic'

License

MIT License

Process

`Name`	`VARSCAN_PROCESSSOMATIC`

Input 1 channel

#1 tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1' ]`
`vcf` file	VCF file `*.{snvs,indels}.vcf.gz`

Output 7 channels

#1 loh_vcf tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1' ]`
`*.LOH.vcf.gz` file	VCF file with loss of heterozygosity variants `*.LOH.vcf.gz`

#2 versions

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

#3 loh_hc_vcf tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1' ]`
`*.LOH.hc.vcf.gz` file	VCF file with high-confidence loss of heterozygosity variants `*.LOH.hc.vcf.gz`

#4 somatic_vcf tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1' ]`
`*.Somatic.vcf.gz` file	VCF file with somatic variants `*.Somatic.vcf.gz`

#5 germline_vcf tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1' ]`
`*.Germline.vcf.gz` file	VCF file with germline variants `*.Germline.vcf.gz`

#6 somatic_hc_vcf tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1' ]`
`*.Somatic.hc.vcf.gz` file	VCF file with high-confidence somatic variants `*.Somatic.hc.vcf.gz`

#7 germline_hc_vcf tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1' ]`
`*.Germline.hc.vcf.gz` file	VCF file with high-confidence germline variants `*.Germline.hc.vcf.gz`

Tool	Description	Homepage
varscan	variant detection in massively parallel sequencing data	https://github.com/dkoboldt/varscan

Version	0.0.0-0c7146d
Commit ID	135d883a43b1a2324b4112cd270cf22e20835533
Release Date	08 Apr 2026 19:21:23 (UTC)
Download URL	https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Fvarscan%2Fprocesssomatic/0.0.0-0c7146d/download
OCI Store URL	https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/varscan/processsomatic/blobs/sha256:7a2c78728bd738be5c73c0fdf3a759ff1f2583dcf2f8e3d1a84e12ba9547e437
Size	3.2 KB
Checksum	sha256:7a2c78728bd738be5c73c0fdf3a759ff1f2583dcf2f8e3d1a84e12ba9547e437
Downloads	1

Version	Date	Status	Downloads	Size	Diff
0.0.0-0c7146d