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!