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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.

SUBMITTER: Hickey G

PROVIDER: S-EPMC7017486 | biostudies-literature | 2020 Feb

REPOSITORIES: biostudies-literature

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Genotyping structural variants in pangenome graphs using the vg toolkit.

Hickey Glenn G Heller David D Monlong Jean J Sibbesen Jonas A JA Sirén Jouni J Eizenga Jordan J Dawson Eric T ET Garrison Erik E Novak Adam M AM Paten Benedict B

Genome biology 20200212 1

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 s ...[more]

PMID: 32051000

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