Graphtyper enables population-scale genotyping using pangenome graphs View Full Text


Ontology type: schema:ScholarlyArticle     


Article Info

DATE

2017-11

AUTHORS

Hannes P Eggertsson, Hakon Jonsson, Snaedis Kristmundsdottir, Eirikur Hjartarson, Birte Kehr, Gisli Masson, Florian Zink, Kristjan E Hjorleifsson, Aslaug Jonasdottir, Adalbjorg Jonasdottir, Ingileif Jonsdottir, Daniel F Gudbjartsson, Pall Melsted, Kari Stefansson, Bjarni V Halldorsson

ABSTRACT

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. More... »

PAGES

1654-1660

References to SciGraph publications

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  • Identifiers

    URI

    http://scigraph.springernature.com/pub.10.1038/ng.3964

    DOI

    http://dx.doi.org/10.1038/ng.3964

    DIMENSIONS

    https://app.dimensions.ai/details/publication/pub.1091911912

    PUBMED

    https://www.ncbi.nlm.nih.gov/pubmed/28945251


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