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dc.contributor.authorEggertsson, Hannes P
dc.contributor.authorJonsson, Hakon
dc.contributor.authorKristmundsdottir, Snaedis
dc.contributor.authorHjartarson, Eirikur
dc.contributor.authorKehr, Birte
dc.contributor.authorMasson, Gisli
dc.contributor.authorZink, Florian
dc.contributor.authorHjorleifsson, Kristjan E
dc.contributor.authorJonasdottir, Aslaug
dc.contributor.authorJonasdottir, Adalbjorg
dc.contributor.authorJonsdottir, Ingileif
dc.contributor.authorGudbjartsson, Daniel F
dc.contributor.authorMelsted, Pall
dc.contributor.authorStefansson, Kari
dc.contributor.authorHalldorsson, Bjarni V
dc.date.accessioned2018-03-22T14:37:48Z
dc.date.available2018-03-22T14:37:48Z
dc.date.issued2017-11
dc.date.submitted2018
dc.identifier.citationGraphtyper enables population-scale genotyping using pangenome graphs. 2017, 49 (11):1654-1660 Nat. Genet.en
dc.identifier.issn1546-1718
dc.identifier.pmid28945251
dc.identifier.doi10.1038/ng.3964
dc.identifier.urihttp://hdl.handle.net/2336/620514
dc.descriptionTo access publisher's full text version of this article click on the hyperlink belowen
dc.description.abstractA fundamental requirement for genetic studies is an accurate determination of sequence variation. While human genome sequence diversity is increasingly well characterized, there is a need for efficient ways to use this knowledge in sequence analysis. Here we present Graphtyper, a publicly available novel algorithm and software for discovering and genotyping sequence variants. Graphtyper realigns short-read sequence data to a pangenome, a variation-aware graph structure that encodes sequence variation within a population by representing possible haplotypes as graph paths. Our results show that Graphtyper is fast, highly scalable, and provides sensitive and accurate genotype calls. Graphtyper genotyped 89.4 million sequence variants in the whole genomes of 28,075 Icelanders using less than 100,000 CPU days, including detailed genotyping of six human leukocyte antigen (HLA) genes. We show that Graphtyper is a valuable tool in characterizing sequence variation in both small and population-scale sequencing studies.
dc.language.isoenen
dc.publisherNature Publishing Groupen
dc.relation.urlhttps://www.nature.com/articles/ng.3964.pdfen
dc.rightsArchived with thanks to Nature geneticsen
dc.subjectGenen
dc.subjectHugbúnaðuren
dc.subjectForriten
dc.subjectAAI12en
dc.subject.meshAlgorithmsen
dc.subject.meshAllelesen
dc.subject.meshBase Sequenceen
dc.subject.meshComputer Graphicsen
dc.subject.meshGenome, Humanen
dc.subject.meshGenotyping Techniquesen
dc.subject.meshHLA Antigensen
dc.subject.meshHaplotypesen
dc.subject.meshHigh-Throughput Nucleotide Sequencingen
dc.subject.meshHumansen
dc.subject.meshPolymorphism, Single Nucleotideen
dc.subject.meshSequence Alignmenten
dc.subject.meshSequence Analysis, DNAen
dc.subject.meshSoftwareen
dc.titleGraphtyper enables population-scale genotyping using pangenome graphs.en
dc.typeArticleen
dc.contributor.department1 ] deCODE Genet Amgen Inc, Reykjavik, Iceland Show more [ 2 ] Univ Iceland, Sch Engn & Nat Sci, Reykjavik, Iceland Show more [ 3 ] Reykjavik Univ, Sch Sci & Engn, Reykjavik, Iceland [ 4 ] BIH, Berlin, Germany Show more [ 5 ] Univ Iceland, Sch Hlth Sci, Fac Med, Reykjavik, Icelanden
dc.identifier.journalNature geneticsen
dc.rights.accessNational Consortium - Landsaðganguren
dc.departmentcodeAAI12
html.description.abstractA fundamental requirement for genetic studies is an accurate determination of sequence variation. While human genome sequence diversity is increasingly well characterized, there is a need for efficient ways to use this knowledge in sequence analysis. Here we present Graphtyper, a publicly available novel algorithm and software for discovering and genotyping sequence variants. Graphtyper realigns short-read sequence data to a pangenome, a variation-aware graph structure that encodes sequence variation within a population by representing possible haplotypes as graph paths. Our results show that Graphtyper is fast, highly scalable, and provides sensitive and accurate genotype calls. Graphtyper genotyped 89.4 million sequence variants in the whole genomes of 28,075 Icelanders using less than 100,000 CPU days, including detailed genotyping of six human leukocyte antigen (HLA) genes. We show that Graphtyper is a valuable tool in characterizing sequence variation in both small and population-scale sequencing studies.


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