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recombination rate #37

Closed agladstein closed 4 years ago

agladstein commented 6 years ago

Hi Gary,

This is a potentially very obvious question. I'm confused about the -r parameter, which is recombination rate per site per 4N generations. If I have a species with a recombination rate of 4.83 cM/Mb, then should the unscaled per site r = 4.83e-8 per site per 1 generation?

Thanks, Ariella

gchen98 commented 6 years ago

The -r parameter is used exactly the same way as in MS (see ms documentation), except that we don't multiply the per base recombination rate by the segment length as in MS. So in your case specify -r as 4.83e-6 4 N_e

the 4.83 cM/Mb is specified in a file which is specified in the -R parameter. This is for use in regions where crossovers happen more or less frequently per segment length.

On 09/14/2017 03:53 PM, agladstein wrote:

Hi Gary,

This is a potentially very obvious question. I'm confused about the -r parameter, which is recombination rate per site per 4N generations. If I have a species with a recombination rate of 4.83 cM/Mb, then should the unscaled per site r = 4.83e-6 per site per 1 generation?

Thanks, Ariella

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