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
Description
Pattern

0 ()

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Output

Name
Description
Pattern

annotated_vcf ()

index ()

versions ()

Tools

gatk4 Documentation

Genome Analysis Toolkit (GATK4)

https://github.com/broadinstitute/gatkdoi: 10.1158/1538-7445.AM2017-3590License: BSD-3-clause
Authors