Where To Get The Genetic Map For The Composite Of Multiple Signals Test

Question

[bmuchmore]

Hello all,

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.

Answer 1

[Giovanni M Dall'Olio]

This folder of the 1000 Genomes website contains the recombination rates by population, instead of continental group:

• ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/working/20130507_omni_recombination_rates/

Note that these data are in the "technical" folder of the ftp, which contains results that are still not definitive. So, use it with care: it may be a good idea to contact the author of these annotations and ask him about how much they are reliable.

In any case, if you are calculating the CMS for all the populations separately, which demographic model are you going to use for the simulations? Which parameters are you going to use for everything that is not CEU, YRI or CHB/JPT?

[Adam]

Just to follow up, the rates that Giovanni referred to are generated from OMNI genotype data. My feeling is that they look pretty reasonable, but I would also emphasize that they have not been subjected to the same degree of analysis as the HapMap rates. The HapMap data also includes a higher SNP density compared to the OMNI array.

[bmuchmore]

Great, thanks for the response. I wonder how I missed that on the 1KG website.

Giovanni, those are excellent questions. The short answer is I have no idea. I will gladly update you if I make significant progress, however. Also, from reading a previous post, I see that if you have been down this road before. Any specific suggestions you want to add before I start pulling my hair out?