So, I have been trying to implement the CMS code (http://www.broadinstitute.org/scientific-community/science/programs/medical-and-population-genetics/cms/code) in order to search for signals of positive selection in a 20,000 bp window for each of the phase 1 1000 genomes populations. However, I don't know where to find or how to generate the following prerequisite:
3.3 Genetic map
Semantic content: For a list of genomic positions, the probability of recombination between that position and the start of the chromosome, per generation.
I think they use the HapMap phase II genetic map, but I want something more up-to-date than that and for each of the populations as opposed to just CEU, YRI and CHB/JPT. I would be very grateful for any pertinent information.
Thank you very much in advance.