Truvari: refined structural variant comparison preserves allelic diversity

• Published in: Genome Biology Vol. 23; no. 1; pp. 271 - 20
• Main Authors: English, Adam C, Menon, Vipin K, Gibbs, Richard A, Metcalf, Ginger A, Sedlazeck, Fritz J
• Format: Journal Article
• Language: English
• Published: England BioMed Central 27-12-2022; BMC
• Subjects: Algorithms; Alleles; Benchmarking; Gene Frequency; Genome, Human; Genomic Structural Variation; High-Throughput Nucleotide Sequencing; Humans; Method; Structural variation; SV annotation; SV benchmarking; SV comparison; SV merging; SV annotation; SV merging; SV benchmarking; Structural variation; SV comparison
• ISSN: 1474-760X; 1474-7596; 1474-760X
• DOI: 10.1186/s13059-022-02840-6

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.