Article
Minimal positional substring cover is a haplotype threading alternative to Li and Stephens model.
Genome research - 1 Jul 2023
Sanaullah Ahsan, Zhi Degui, Zhang Shaojie
Abstract excerpt
The Li and Stephens (LS) hidden Markov model (HMM) models the process of reconstructing a haplotype as a mosaic copy of haplotypes in a reference panel. For small panels, the probabilistic parameterization of LS enables modeling the uncertainties of such mosaics. However, LS becomes inefficient when sample size is large, because of its linear time complexity. Recently the PBWT, an efficient data structure...
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