Package org.broadinstitute.hellbender.tools.walkers.sv
package org.broadinstitute.hellbender.tools.walkers.sv
-
ClassesClassDescriptionCreates discordant read pair, split read evidence, site depth, and read depth files for use in the GATK-SV pipeline.Merge GCNV segments VCFs This tool takes in segmented VCFs produced by
PostprocessGermlineCNVCalls.Adds gene overlap, predicted functional consequence, and noncoding element overlap annotations to a structural variant (SV) VCF from the GATK-SV pipeline.Clusters structural variants based on coordinates, event type, and supporting algorithms.This tool calculates SV genotype concordance between an "evaluation" VCF and a "truth" VCF.