Abstract
MOTIVATION: The availability of large genotyped cohorts brings new opportunities for revealing the high-resolution genetic structure of admixed populations via local ancestry inference (LAI), the process of identifying the ancestry of each segment of an individual haplotype. Though current methods achieve high accuracy in standard cases, LAI is still challenging when reference populations are more similar (e.g. intra-continental), when the number of reference populations is too numerous, or when the admixture events are deep in time, all of which are increasingly unavoidable in large biobanks. RESULTS: In this work, we present Recomb-Mix, a new LAI method which integrates elements from the site-based Li and Stephens model and introduces a new graph collapsing techniques to simplify counting paths with the same ancestry label readout. Through comprehensive benchmarking on various simulated datasets, we show that Recomb-Mix is more accurate than existing methods in diverse sets of scenarios while being competitive in terms of resource efficiency. The scalability and robustness of Recomb-Mix are also demonstrated with real-world datasets. We expect that Recomb-Mix will be a useful method for advancing genetics studies of admixed populations. AVAILABILITY AND IMPLEMENTATION: The implementation of Recomb-Mix is available at https://github.com/ucfcbb/Recomb-Mix.