Description

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.

Input

name:type
description
pattern

meta:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end

]

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

fasta:file

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

*.{fasta,fa}

fasta_fai:file

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

*.fai

dict:file

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

*.dict

Output

name:type
description
pattern

annotated_vcf

meta:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end

]

*.vcf.gz:file

The annotated structural variant VCF

*.vcf.gz

index

meta:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end

]

*.vcf.gz.tbi:file

The index of the VCF

*.vcf.gz.tbi

versions

versions.yml:file

File containing software versions

versions.yml

Tools

maintainer
Github user nvnieuwk
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