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dc.contributor.authorHickey, Glenn
dc.contributor.authorHeller, David
dc.contributor.authorMonlong, Jean
dc.contributor.authorSibbesen, Jonas A
dc.contributor.authorSirén, Jouni
dc.contributor.authorEizenga, Jordan
dc.contributor.authorDawson, Eric T
dc.contributor.authorGarrison, Erik
dc.contributor.authorNovak, Adam M
dc.contributor.authorPaten, Benedict
dc.date.accessioned2021-02-11T16:17:20Z
dc.date.available2021-02-11T16:17:20Z
dc.date.issued2020-02-12
dc.date.submitted2019-05-31
dc.identifier.issn1474-7596
dc.identifier.others13059-020-1941-7
dc.identifier.other1941
dc.identifier.urihttps://www.repository.cam.ac.uk/handle/1810/317501
dc.description.abstractStructural 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.
dc.languageen
dc.publisherSpringer Science and Business Media LLC
dc.rightsAttribution 4.0 International (CC BY 4.0)
dc.rights.urihttps://creativecommons.org/licenses/by/4.0/
dc.subjectMethod
dc.subjectGraph genomes
dc.titleGenotyping structural variants in pangenome graphs using the vg toolkit.
dc.typeArticle
dc.date.updated2021-02-11T16:17:20Z
prism.issueIdentifier1
prism.publicationNameGenome Biol
prism.volume21
dc.identifier.doi10.17863/CAM.64617
dcterms.dateAccepted2020-01-20
rioxxterms.versionofrecord10.1186/s13059-020-1941-7
rioxxterms.versionVoR
rioxxterms.licenseref.urihttp://creativecommons.org/licenses/by/4.0/
dc.identifier.eissn1474-760X
pubs.funder-project-idNational Human Genome Research Institute (U54HG007990, U01HL137183, 2U41HG007234)
pubs.funder-project-idW. M. Keck Foundation (DT06172015)
pubs.funder-project-idSimons Foundation (SFLIFE# 35190)
cam.issuedOnline2020-02-12


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Attribution 4.0 International (CC BY 4.0)
Except where otherwise noted, this item's licence is described as Attribution 4.0 International (CC BY 4.0)