The solution surface of the Li-Stephens haplotype copying model.

ABSTRACT: The Li-Stephens (LS) haplotype copying model forms the basis of a number of important statistical inference procedures in genetics. LS is a probabilistic generative model which supposes that a sampled chromosome is an imperfect mosaic of other chromosomes found in a population. In the frequentist setting which is the focus of this paper, the output of LS is a "copying path" through chromosome space. The behavior of LS depends crucially on two user-specified parameters, [Formula: see text] and [Formula: see text], which are respectively interpreted as the rates of mutation and recombination. However, because LS is not based on a realistic model of ancestry, the precise connection between these parameters and the biological phenomena they represent is unclear. Here, we offer an alternative p

SUBMITTER: Jin Y 

PROVIDER: S-EPMC10410957 | biostudies-literature | 2023 Aug

REPOSITORIES: biostudies-literature