Motivation: Recombination rates vary considerably at the fine scale within mammalian genomes, with the majority of recombination occurring within hotspots of ~2 kb in width. We present a method for inferring the location of recombination hotspots from patterns of linkage disequilibrium within samples of population genetic data. Results: Using simulations, we show that our method has hotspot detection power of approximately 50-60%, but depending on the magnitude of the hotspot. The false positive rate is between 0.24 and 0.56 false positives per Mb for data typical of humans. Availability: http://github.com/auton1/LDhot
@article{arxiv.1403.4264,
title = {Identifying recombination hotspots using population genetic data},
author = {Adam Auton and Simon Myers and Gil McVean},
journal= {arXiv preprint arXiv:1403.4264},
year = {2014}
}