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

Author:

Aslett Louis J. M.,Christ Ryan R.

Abstract

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 $$N \times N$$ 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 . kalis enables investigators to rapidly resolve the ancestry at loci of interest and developers to build a range of variant-specific ancestral inference pipelines on top. kalis exploits both multi-core parallelism and modern CPU vector instruction sets to enable scaling to hundreds of thousands of genomes. Conclusions The resulting distance matrices accessible via kalis enable local ancestry, selection, and association studies in modern large scale genomic datasets.

Funder

NHGRI Centers for Common Disease Genomics

Publisher

Springer Science and Business Media LLC

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