Kalis: a modern implementation of the Li & Stephens model for local ancestry inference in R.

ABSTRACT:

Background

Approximating the recent phylogeny of N phased haplotypes at a set of variants along the genome is a core problem in modern population genomics and central to performing genome-wide screens for association, selection, introgression, and other signals. The Li & Stephens (LS) model provides a simple yet powerful hidden Markov model for inferring the recent ancestry at a given variant, represented as an N × N distance matrix based on posterior decodings.

Results

We provide a high-performance engine to make these posterior decodings readily accessible with minimal pre-processing via an easy to use package kalis, in the statistical programming language R. kalis enables investigators to rapidly resolve the ancestry at loci of interest and developers to build a range of

SUBMITTER: Aslett LJM 

PROVIDER: S-EPMC10900616 | biostudies-literature | 2024 Feb

REPOSITORIES: biostudies-literature