Truvari: Refined Structural Variant Comparison Preserves Allelic Diversity

Authors

Adam C English
Vipin K Menon
Richard A Gibbs
Ginger A Metcalf
Fritz J Sedlazeck

Language

English

Publication Date

12-27-2022

Journal

Genome Biology

DOI

10.1186/s13059-022-02840-6

PMID

36575487

PMCID

PMC9793516

PubMedCentral® Posted Date

12-27-2022

PubMedCentral® Full Text Version

Post-print

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.

Keywords

Humans, Genomic Structural Variation, Gene Frequency, Algorithms, Alleles, Benchmarking, High-Throughput Nucleotide Sequencing, Genome, Human, Structural variation, SV comparison, SV merging, SV benchmarking, SV annotation

Published Open-Access

yes

Recommended Citation

English, Adam C; Menon, Vipin K; Gibbs, Richard A; et al., "Truvari: Refined Structural Variant Comparison Preserves Allelic Diversity" (2022). Faculty and Staff Publications. 5108.
https://digitalcommons.library.tmc.edu/baylor_docs/5108