nf-core/variantextractor @ 0.0.0-0c7146d
Summary
Deterministic and standard extractor of SNVs, indels and structural variants (SVs) from VCF files. Homogenizes multiallelic variants, MNPs and SVs (including imprecise paired breakends and single breakends) to facilitate downstream processing.
Get started
Add the following snippet to your workflow script to include this module.
include { VARIANTEXTRACTOR } from 'nf-core/variantextractor'
License
MIT License
Process
Name
|
VARIANTEXTRACTOR |
|---|
Input
1 channel
#1
tuple
meta
map
|
Groovy Map containing sample information. e.g. [ id:'sample1' ] |
|---|---|
vcf
file
|
Input VCF file containing variants to be extracted and homogenized. *.{vcf,vcf.gz}
|
Output
2 channels
#1
vcf
tuple
meta
map
|
Groovy Map containing sample information. e.g. [ id:'sample1' ] |
|---|---|
*.vcf
file
|
VCF file with variants extracted and homogenized (multiallelic split, MNPs decomposed, SV breakends deduplicated). *.vcf
|
#2
versions_variantextractor
versions.yml
file
|
File containing software versions. versions.yml
|
|---|
| Tool | Description | Homepage |
|---|---|---|
| variant-extractor | Deterministic and standard extractor of SNVs, indels and structural variants from VCF files built under the frame of EUCANCan. | https://github.com/EUCANCan/variant-extractor |
| Version | 0.0.0-0c7146d |
|---|---|
| Commit ID | 135d883a43b1a2324b4112cd270cf22e20835533 |
| Release Date | 08 Apr 2026 19:21:14 (UTC) |
| Download URL | https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Fvariantextractor/0.0.0-0c7146d/download |
| OCI Store URL | https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/variantextractor/blobs/sha256:1de80b394cafc6484d02d789699705a7b8c41160f4bcabc213d647dc69c8abb8 |
| Size | 2.7 KB |
| Checksum | sha256:1de80b394cafc6484d02d789699705a7b8c41160f4bcabc213d647dc69c8abb8 |
| Downloads | 1 |
| Version | Date | Status | Downloads | Size | Diff |
|---|---|---|---|---|---|
| 0.0.0-0c7146d | 08 Apr 2026 19:21:14 (UTC) | 1 | 2.7 KB | - |