Genetic map distances

As the haplotype pattern in the sample is the result of recombination events in the ancestry of the sample, specifying the precise recombination rate (genetic distance) between markers improves the quality of the results. While the physical location of the markers provides the simplest estimate, it is now becoming clear that recombination rates can vary greatly over short physical distances. Therefore, we suggest the use of a statistical model to estimate the intermarker recombination rates and apply those rates instead of the physical distances (for example Li and Stephens, 2003; McVean et al., 2004). These programs will provide relative recombination rates between markers. By replacing the intermarker distances with these relative rates, a more precise genetic map of the region of interest will be used. As TreeLD estimates the regionwide recombination rate as a nuisance parameter, it is not necessary to provide the absolute genetic distances in the sample, as long as the relative genetic distances are correct.