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Genotyping structural variants in pangenome graphs using the vg toolkit

Published version
Peer-reviewed

Change log

Authors

Hickey, Glenn 
Heller, David 
Monlong, Jean 
Sibbesen, Jonas A. 
Sirén, Jouni 

Abstract

Abstract: Structural variants (SVs) remain challenging to represent and study relative to point mutations despite their demonstrated importance. We show that variation graphs, as implemented in the vg toolkit, provide an effective means for leveraging SV catalogs for short-read SV genotyping experiments. We benchmark vg against state-of-the-art SV genotypers using three sequence-resolved SV catalogs generated by recent long-read sequencing studies. In addition, we use assemblies from 12 yeast strains to show that graphs constructed directly from aligned de novo assemblies improve genotyping compared to graphs built from intermediate SV catalogs in the VCF format.

Description

Keywords

Method, Graph genomes

Journal Title

Genome Biology

Conference Name

Journal ISSN

1474-760X

Volume Title

21

Publisher

BioMed Central
Sponsorship
National Human Genome Research Institute (U54HG007990, U01HL137183, 2U41HG007234)
W. M. Keck Foundation (DT06172015)
Simons Foundation (SFLIFE# 35190)