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Haplotype-aware graph indexes

By Jouni Sirén, Erik Garrison, Adam M. Novak, Benedict Paten, Richard Durbin

Posted 24 Feb 2019
bioRxiv DOI: 10.1101/559583 (published DOI: 10.1093/bioinformatics/btz575)

Motivation: The variation graph toolkit (VG) represents genetic variation as a graph. Although each path in the graph is a potential haplotype, most paths are nonbiological, unlikely recombinations of true haplotypes. Results: We augment the VG model with haplotype information to identify which paths are more likely to exist in nature. For this purpose, we develop a scalable implementation of the graph extension of the positional Burrows--Wheeler transform (GBWT). We demonstrate the scalability of the new implementation by building a whole-genome index of the 5,008 haplotypes of the 1000 Genomes Project, and an index of all 108,070 TOPMed Freeze 5 chromosome 17 haplotypes. We also develop an algorithm for simplifying variation graphs for k-mer indexing without losing any k-mers in the haplotypes.

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