Truvari: Refined Structural Variant Comparison Preserves Allelic Diversity

For multi-sample structural variant analyses like merging, benchmarking, and annotation, the fundamental operation is to identify when two SVs are the same. Commonly applied approaches for comparing SVs were developed alongside technologies which produce ill-defined boundaries. As SV detection becomes more exact, algorithms to preserve this refined signal are needed. Here we present Truvari - a SV comparison, annotation and analysis toolkit - and demonstrate the effect of SV comparison choices by building population-level VCFs from 36 haplotype-resolved long-read assemblies. We observe over-merging from other SV merging approaches which causes up to a 2.2x inflation of allele frequency relative to Truvari.