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

meta (map)

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

]

versions (file)

File containing software versions

versions.yml

annotated_vcf (file)

The annotated structural variant VCF

*.vcf.gz

index (file)

The index of the VCF

*.vcf.gz.tbi
maintainer
Github user nvnieuwk
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