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Motivation: Recombination rates vary considerably at the fine scale withinmammalian genomes, with the majority of recombination occurring within hotspotsof ~2 kb in width. We present a method for inferring the location ofrecombination hotspots from patterns of linkage disequilibrium within samplesof population genetic data. Results: Using simulations, we show that our methodhas hotspot detection power of approximately 50-60%, but depending on themagnitude of the hotspot. The false positive rate is between 0.24 and 0.56false positives per Mb for data typical of humans. Availability:http://github.com/auton1/LDhot

Identifying recombination hotspots using population genetic data