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Genotyping structural variants in pangenome graphs using the vg toolkit

2020; BioMed Central; Volume: 21; Issue: 1 Linguagem: Inglês

10.1186/s13059-020-1941-7

1474-760X

Glenn Hickey, David N. Heller, Jean Monlong, Jonas A. Sibbesen, Jouni Sirén, Jordan M. Eizenga, Eric T. Dawson, Erik Garrison, Adam M. Novak, Benedict Paten,

Evolution and Genetic Dynamics

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.