Truvari: refined structural variant comparison preserves allelic diversity.

TitleTruvari: refined structural variant comparison preserves allelic diversity.
Publication TypeJournal Article
Year of Publication2022
AuthorsEnglish, AC, Menon, V, Gibbs, RA, Metcalf, GA, Sedlazeck, FJ
JournalGenome Biol
Date Published2022 Dec 27
KeywordsAlgorithms, Alleles, Benchmarking, Gene Frequency, Genome, Human, Genomic Structural Variation, High-Throughput Nucleotide Sequencing, Humans

The fundamental challenge of multi-sample structural variant (SV) analysis such as merging and benchmarking is identifying when two SVs are the same. Common 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-an 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 cause up to a 2.2× inflation of allele frequency, relative to Truvari.

Alternate JournalGenome Biol
PubMed ID36575487
PubMed Central IDPMC9793516
Grant ListUM1 HG008898 / HG / NHGRI NIH HHS / United States