Haplotype-aware graph indexes
Haplotype-aware graph indexes
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DOI：
10.1093/bioinformatics/btz575
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发表时间：
2020-01-15
期刊：
影响因子：
5.8
通讯作者：
Durbin, Richard
中科院分区：
文献类型：
--
作者：
Siren, Jouni;Garrison, Erik;Durbin, Richard
动机：变异图表工具包(VG)将遗传变异表示为图表。虽然图中的每条路径都是潜在的单倍型，但大多数路径都是真实单倍型的非生物、不太可能的重组。结果：我们用单倍型信息增强了VG模型，以确定哪些路径更有可能存在于自然界中。为此，我们开发了位置Burrow-Wheeler变换的图形扩展的可伸缩实现。我们通过建立1000基因组计划的5008个单倍型的全基因组索引和精确医学冷冻5号染色体17号染色体的所有108 070个跨基因组单倍型的索引，展示了新实现的可扩展性。我们还开发了一种简化k-mer索引的变异图的算法，而不会丢失单倍型中的任何k-mer。
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 non-biological, 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. We demonstrate the scalability of the new implementation by building a whole-genome index of the 5008 haplotypes of the 1000 Genomes Project, and an index of all 108 070 Trans-Omics for Precision Medicine 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.