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

nf-core/varscan/fpfilter @ 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. Subtool fpfilter is used to filter a set of SNPs/indels based on coverage, reads, p-value, etc.

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_FPFILTER } from 'nf-core/varscan/fpfilter'

License

MIT License

Process

`Name`	`VARSCAN_FPFILTER`

Input 1 channel

#1 tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1' ]`
`vcf` file	VCF file `*.vcf.gz`
`rc` file	Read counts file from bam-readcount `*.rc`

Output 3 channels

#1 fail_vcf tuple

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

#2 pass_vcf tuple

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

#3 versions

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

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 19:21:22 (UTC)
Download URL	https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Fvarscan%2Ffpfilter/0.0.0-0c7146d/download
OCI Store URL	https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/varscan/fpfilter/blobs/sha256:1ff397e51a8ddeeae657ce4dc118217edb7538198bc00beb3b6d9ee23b1bbd19
Size	3.3 KB
Checksum	sha256:1ff397e51a8ddeeae657ce4dc118217edb7538198bc00beb3b6d9ee23b1bbd19
Downloads	1

Version	Date	Status	Downloads	Size	Diff
0.0.0-0c7146d	08 Apr 2026 19:21:22 (UTC)		1	3.3 KB	-