The haplotype on which a beneficial allele resides tends to be significantly longer than the other haplotypes at the same frequency in the population when adjusted for the recombination background. However, long haplotypes tend to occur in regions with low recombination, and these can be confused with genuine genomic signals of positive selection [38]. This is why WHAMM attempts to control for recombination by requiring the input of a cM map. The map we used here was the cM map for imputation available on the website for the program SHAPEIT2.
