TY - JOUR T1 - Graphtyper: Population-scale genotyping using pangenome graphs JF - bioRxiv DO - 10.1101/148403 SP - 148403 AU - Hannes P. Eggertsson AU - Hakon Jonsson AU - Snaedis Kristmundsdottir AU - Eirikur Hjartarson AU - Birte Kehr AU - Gisli Masson AU - Florian Zink AU - Aslaug Jonasdottir AU - Adalbjorg Jonasdottir AU - Ingileif Jonsdottir AU - Daniel F. Gudbjartsson AU - Pall Melsted AU - Kari Stefansson AU - Bjarni V. Halldorsson Y1 - 2017/01/01 UR - http://biorxiv.org/content/early/2017/06/09/148403.abstract N2 - A fundamental requisite 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 utilize 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 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 population-scale sequencing studies. ER -