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Nat Genet. 2017 Nov;49(11):1654-1660. doi: 10.1038/ng.3964. Epub 2017 Sep 25.

Graphtyper enables population-scale genotyping using pangenome graphs.

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deCODE Genetics/Amgen, Inc., Reykjavik, Iceland.
School of Engineering and Natural Sciences, University of Iceland, Reykjavik, Iceland.
School of Science and Engineering, Reykjavik University, Reykjavik, Iceland.
Berlin Institute of Health (BIH), Berlin, Germany.
Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland.


A 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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