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nf-core/gatk4/svannotate @ 0.0.0-0c7146d

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: 0.0.0-0c7146d
Total downloads: 1
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 0.0.0-0c7146d
Commit ID 135d883a43b1a2324b4112cd270cf22e20835533
Release Date 08 Apr 2026 18:43:17 (UTC)
Download URL https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Fgatk4%2Fsvannotate/0.0.0-0c7146d/download
OCI Store URL https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/gatk4/svannotate/blobs/sha256:f713353fb0985c8011ad3a33e057d32f32a7d95a3f5c92b66de64e6c53486ee8