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nf-core/gatk4/svannotate @ 0.0.0-6c4ed3a

Adds predicted functional consequence, gene overlap, and noncoding element overlap annotations to SV VCF from GATK-SV pipeline. Input files are an SV VCF, a GTF file containing primary or canonical transcripts, and a BED file containing noncoding elements. Output file is an annotated SV VCF.

annotate gatk4 structural variants svannotate vcf
Latest version: 0.0.0-6c4ed3a
Total downloads: 6
Source: nf-core/modules
Authors: @nvnieuwk
Maintainers: @nvnieuwk

Summary

Adds predicted functional consequence, gene overlap, and noncoding element overlap annotations to SV VCF from GATK-SV pipeline. Input files are an SV VCF, a GTF file containing primary or canonical transcripts, and a BED file containing noncoding elements. Output file is an annotated SV VCF.

Get started

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

include { GATK4_SVANNOTATE } from 'nf-core/gatk4/svannotate'

License

MIT License

Process
Name GATK4_SVANNOTATE
Input 5 channels
#1 tuple
meta map

Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
vcf file

A VCF file created with a structural variant caller

 *.vcf.gz
tbi file

The index file of the VCF

 *.vcf.gz.tbi
bed file

Regions to limit the analysis to

 *.bed
non_coding_bed file

File containing noncoding regions

 *.bed
#2 tuple
meta2 map

Groovy Map containing FASTA information e.g. [ id:'test', single_end:false ]
fasta file

Optional - reference FASTA file needed when the input is a CRAM file

 *.{fasta,fa}
#3 tuple
meta3 map

Groovy Map containing FAI information e.g. [ id:'test', single_end:false ]
fasta_fai file

Optional - index of the reference FASTA file needed when the input is a CRAM file

 *.fai
#4 tuple
meta4 map

Groovy Map containing DICT information e.g. [ id:'test', single_end:false ]
dict file

Optional - sequence dictionary of the reference FASTA file needed when the input is a CRAM file

 *.dict
#5 tuple
meta5 map

Groovy Map containing GTF information e.g. [ id:'test', single_end:false ]
gtf file

Optional - GTF file containing transcript information

 *.gtf
Output 3 channels
#1 tbi tuple
meta map

Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
*.vcf.gz.tbi file

The index of the VCF

 *.vcf.gz.tbi
#2 vcf tuple
meta map

Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
*.vcf.gz file

The annotated structural variant VCF

 *.vcf.gz
#3 versions_gatk4 tuple
${task.process} string

The name of the process
gatk4 string

The name of the tool
gatk --version | sed -n '/GATK.*v/s/.*v//p' eval

The expression to obtain the version of the tool
Tool Description Homepage
gatk4 Genome Analysis Toolkit (GATK4) https://gatk.broadinstitute.org/hc/en-us
Version 0.0.0-6c4ed3a
Commit ID 6c4ed3a220310b905a1fc9d04f05be2e0837142b
Release Date 23 Apr 2026 15:20:38 (UTC)
Download URL https://registry.nextflow.io/api/v1/modules/nf-core%2Fgatk4%2Fsvannotate/0.0.0-6c4ed3a/download
OCI Store URL https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/gatk4/svannotate/blobs/sha256:80386e6d1131ed40ad57cf562d63747d9eaa683bd63f319eb8858cb6589b840a