Question: Recombination rates for phasing & imputation
gravatar for Shab86
2.3 years ago by
Shab86240 wrote:

I am using LDHAT to calculate a population-specific recombination map. The output from LDHAT gives rho values (population recombination rate) on a per-position basis. However, to use this genetic map for phasing or imputation, I need the values in cM/Mb. For example, the genetic map used in phasing:

chr   position     RECOMB_rate(cM/Mb)     Genetic_Map(cM)
1     20014981        0.0000000000       0.000000000000
1     20049831        0.1031918738       0.003596236802
1     20055634        0.1032565516       0.004195434571

Would I be correct in assuming that I should multiply rho by 100/(4*Ne) and then divide this quantity with the difference between current & next position? For example, LDHAT output:

Position    Rho
100          1
101          2


per-generation rate (cM/Mb) at position 100 = [1*100/(4*Ne)]cM / [(101–100)*10^-6Mb]

Also, are the genetic positions (cM) in those maps then calculated in a cumulative fashion i.e., To get genetic position for physical position 101, we add up the cM values of 100 and 101?

Any help would be greatly appreciated!

genomics recombination ldhat • 1.1k views
ADD COMMENTlink modified 5 months ago by james0 • written 2.3 years ago by Shab86240
gravatar for james
5 months ago by
james0 wrote:

did you get any where with this?

ADD COMMENTlink written 5 months ago by james0
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