FastRecomb: Fast inference of genetic recombination rates in biobank scale data

Abstract

While rates of recombination events across the genome (genetic maps) are fundamental to genetic research, the majority of current studies only use one standard map. There is evidence suggesting population differences in genetic maps, and thus estimating population-specific maps are of interest. While the recent availability of biobank-scale data offers such opportunities, current methods are not efficient at leveraging very large sample sizes. The most accurate methods are still linkage-disequilibrium (LD)-based methods that are only tractable for a few hundred samples. In this work, we propose a fast and memory-efficient method for estimating genetic maps from population genotyping data. Our method, FastRecomb, leverages the efficient positional Burrows-Wheeler transform (PBWT) data structure for counting IBD segment boundaries as potential recombination events. We used PBWT blocks to avoid redundant counting of pairwise matches. Moreover, we used a panel smoothing technique to reduce the noise from errors and recent mutations. Using simulation, we found that FastRecomb achieves state-of-the-art performance at 10k resolution, in terms of correlation coefficients between the estimated map and the ground truth. This is mainly due to the fact that FastRecomb can effectively take advantage of large panels comprising more than hundreds of thousands of haplotypes. At the same time, other methods lack the efficiency to handle such data. We believe further refinement of FastRecomb would deliver more accurate genetic maps for the genetics community.