Details

Autor(en) / Beteiligte

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

Titel

Graphtyper enables population-scale genotyping using pangenome graphs

Ist Teil von

• Nature genetics, 2017-11, Vol.49 (11), p.1654-1660

Ort / Verlag

New York: Nature Publishing Group US

Erscheinungsjahr

2017

Quelle

MEDLINE

Beschreibungen/Notizen

• Graphtyper is a fast and scalable method for variant genotyping that aligns short-read sequence data to a pangenome. Graphtyper was able to accurately genotype ∼90 million sequence variants in the whole genomes of ∼28,000 Icelanders, including those in six HLA genes. 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.