Title | Truvari: refined structural variant comparison preserves allelic diversity. |
Publication Type | Journal Article |
Year of Publication | 2022 |
Authors | English, AC, Menon, V, Gibbs, RA, Metcalf, GA, Sedlazeck, FJ |
Journal | Genome Biol |
Volume | 23 |
Issue | 1 |
Pagination | 271 |
Date Published | 2022 Dec 27 |
ISSN | 1474-760X |
Keywords | Algorithms, Alleles, Benchmarking, Gene Frequency, Genome, Human, Genomic Structural Variation, High-Throughput Nucleotide Sequencing, Humans |
Abstract | 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. |
DOI | 10.1186/s13059-022-02840-6 |
Alternate Journal | Genome Biol |
PubMed ID | 36575487 |
PubMed Central ID | PMC9793516 |
Grant List | UM1 HG008898 / HG / NHGRI NIH HHS / United States |