Genotyping structural variants in pangenome graphs using the vg toolkit.

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.

journal_name

Genome Biol

journal_title

Genome biology

authors

Hickey G,Heller D,Monlong J,Sibbesen JA,Sirén J,Eizenga J,Dawson ET,Garrison E,Novak AM,Paten B

doi

10.1186/s13059-020-1941-7

subject

Has Abstract

pub_date

2020-02-12 00:00:00

pages

35

issue

1

eissn

1474-7596

issn

1474-760X

pii

10.1186/s13059-020-1941-7

journal_volume

21

pub_type

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