VCFv4.3 section 5.4.9 defines a single breakend notation which uses . to signify a breakend with an unknown partner. Currently, VariantAnnotation attempts to load these variants as a DNAStringSet which results in ALT of all breakend variants being removed when loading the VCF.
vobencha
commented
6 years ago
VCFv4.3 section 5.4.9 defines a single breakend notation which uses
.to signify a breakend with an unknown partner. Currently, VariantAnnotation attempts to load these variants as a DNAStringSet which results in ALT of all breakend variants being removed when loading the VCF.