nf-core/varscan/fpfilter @ 0.0.0-6c4ed3a
Summary
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.
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. |
|---|---|
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. |
|---|---|
*.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. |
|---|---|
*.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 | 0.0.0-6c4ed3a |
|---|---|
| Commit ID | 6c4ed3a220310b905a1fc9d04f05be2e0837142b |
| Release Date | 23 Apr 2026 15:51:51 (UTC) |
| Download URL | https://registry.nextflow.io/api/v1/modules/nf-core%2Fvarscan%2Ffpfilter/0.0.0-6c4ed3a/download |
| OCI Store URL | https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/varscan/fpfilter/blobs/sha256:59cc7ff42cd0a6cc5174543289942b8c86f105d4c917634d5903db73924ab8a4 |
| Size | 3.3 KB |
| Checksum | sha256:59cc7ff42cd0a6cc5174543289942b8c86f105d4c917634d5903db73924ab8a4 |
| Downloads | 1 |
| Version | Date | Status | Downloads | Size |
|---|---|---|---|---|
| 0.0.0-6c4ed3a | 23 Apr 2026 15:51:51 (UTC) | 1 | 3.3 KB | |
| 0.0.0-0c7146d | 08 Apr 2026 19:45:30 (UTC) | 1 | 3.3 KB |