Haplotype-aware graph indexes
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Publication:5090328
Abstract: The variation graph toolkit (VG) represents genetic variation as a graph. Each path in the graph is a potential haplotype, though most paths are unlikely recombinations of true haplotypes. We augment the VG model with haplotype information to identify which paths are more likely to be correct. 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 indexing the 1000 Genomes Project 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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Cited in
(7)- Vaquita: fast and accurate identification of structural variation using combined evidence
- From de Bruijn graphs to variation graphs -- relationships between pangenome models
- Indexing variation graphs
- Read mapping on genome variation graphs
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- Pangenomic genotyping with the marker array
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