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 Bioljournal_title
Genome biologyauthors
Hickey G,Heller D,Monlong J,Sibbesen JA,Sirén J,Eizenga J,Dawson ET,Garrison E,Novak AM,Paten Bdoi
10.1186/s13059-020-1941-7subject
Has Abstractpub_date
2020-02-12 00:00:00pages
35issue
1eissn
1474-7596issn
1474-760Xpii
10.1186/s13059-020-1941-7journal_volume
21pub_type
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