2-AIN-505, 2-AIN-251: Seminár z bioinformatiky (1) a (3)
Zima 2020

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. Graphtyper enables population-scale genotyping using pangenome graphs. Nature genetics, 49(11):1654-1660. 2017.

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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.