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

Hannes P. Eggertsson, Snaedis Kristmundsdottir, Doruk Beyter, Hakon Jonsson, Astros Skuladottir, Marteinn T. Hardarson, Daniel F. Gudbjartsson, Kari Stefansson, Bjarni V. Halldorsson, Pall Melsted. GraphTyper2 enables population-scale genotyping of structural variation usingpangenome graphs. Nat Commun, 10(1):5402. 2019.

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Analysis of sequence diversity in the human genome is fundamental for genetic
studies. Structural variants (SVs) are frequently omitted in sequence analysis
studies, although each has a relatively large impact on the genome. Here, we
present GraphTyper2, which uses pangenome graphs to genotype SVs and small
variants using short-reads. Comparison to the syndip benchmark dataset shows that
our SV genotyping is sensitive and variant segregation in families demonstrates
the accuracy of our approach. We demonstrate that incorporating public assembly
data into our pipeline greatly improves sensitivity, particularly for large
insertions. We validate 6,812 SVs on average per genome using long-read data of
41 Icelanders. We show that GraphTyper2 can simultaneously genotype tens of
thousands of whole-genomes by characterizing 60 million small variants and half a
million SVs in 49,962 Icelanders, including 80 thousand SVs with high-confidence.