Minimal Positional Substring Cover Is a Haplotype Threading Alternative to LI and Stephens Model

Authors

Ahsan Sanaullah
Degui Zhi
Shaojie Zhang

Publication Date

7-1-2023

Journal

Genome Research

Abstract

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 capturing the local haplotype matching among haplotypes, was proposed to offer a fast method for giving some optimal solution (Viterbi) to the LS HMM. Previously, we introduced the minimal positional substring cover (MPSC) problem as an alternative formulation of LS whose objective is to cover a query haplotype by a minimum number of segments from haplotypes in a reference panel. The MPSC formulation allows the generation of a haplotype threading in time constant to sample size (

Keywords

Humans, Haplotypes, Software, Genotype, Algorithms, Ethnicity

Comments

Supplementary Materials

PMID: 37316352