Add support for breakend replacement alleles in SVCluster #8408
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epiercehoffman
approved these changes
Jul 11, 2023
| final Allele refAllele = collapseRefAlleles(representative.getContigA(), start); | ||
| final List<Allele> altAlleles; | ||
| if (type == GATKSVVCFConstants.StructuralVariantAnnotationType.BND) { | ||
| altAlleles = Collections.singletonList(constructBndAllele(strandA, representative.getStrandB(), representative.getContigB(), end, refAllele)); |
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| altAlleles = Collections.singletonList(constructBndAllele(strandA, representative.getStrandB(), representative.getContigB(), end, refAllele)); | |
| altAlleles = Collections.singletonList(constructBndAllele(strandA, strandB, representative.getContigB(), end, refAllele)); |
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Implements allele collapsing for "breakend replacement" BND alleles, as described in section 5.4 of the VCFv4.2 spec.
Also:
CanonicalSVCollapser.