April 21, 2020  |  

Haplotype-aware diplotyping from noisy long reads.

Authors: Ebler, Jana and Haukness, Marina and Pesout, Trevor and Marschall, Tobias and Paten, Benedict

Current genotyping approaches for single-nucleotide variations rely on short, accurate reads from second-generation sequencing devices. Presently, third-generation sequencing platforms are rapidly becoming more widespread, yet approaches for leveraging their long but error-prone reads for genotyping are lacking. Here, we introduce a novel statistical framework for the joint inference of haplotypes and genotypes from noisy long reads, which we term diplotyping. Our technique takes full advantage of linkage information provided by long reads. We validate hundreds of thousands of candidate variants that have not yet been included in the high-confidence reference set of the Genome-in-a-Bottle effort.

Journal: Genome biology
DOI: 10.1186/s13059-019-1709-0
Year: 2019

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