Truvari: Refined Structural Variant Comparison Preserves Allelic Diversity release_4d5pvniyzngihnzzh5cgnb2agi

by Adam C. English, Vipin K. Menon, Richard Gibbs, Ginger Metcalf, Fritz Sedlazeck

Released as a post by Cold Spring Harbor Laboratory.

2022  

Abstract

<jats:title>Abstract</jats:title>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.
In application/xml+jats format

Archived Files and Locations

application/pdf  1.1 MB
file_tprhos7gbfh4vjlz6nwuo73xkq
www.biorxiv.org (repository)
web.archive.org (webarchive)
application/pdf  1.1 MB
file_v7aajxwxy5a5disgucuq4qwktm
www.biorxiv.org (repository)
web.archive.org (webarchive)
Read Archived PDF
Preserved and Accessible
Type  post
Stage   unknown
Date   2022-02-22
Work Entity
access all versions, variants, and formats of this works (eg, pre-prints)
Catalog Record
Revision: b00b3d9d-9ed1-4ad7-8ed1-8fc1cb463cc9
API URL: JSON