Convert Snp Physical Position(Bp) Into Genetic Distance(Cm)

Question

[zy041225]

All I got are lists of SNPs with their physical positions, now I would like to convert them to genetic distance (centiMorgan) to calculate iHS.

I've donwloaded the latest HapMap II SNPs from http://ftp.hapmap.org/hapmap/recombination/2011-01_phaseII_B37/ but found that there are not enough SNPs I need.

What do you suggest?

Thanks for your help!

[Pierre Lindenbaum]

related:

Position of genes in centiMorgans?

How to convert centimorgan to base pair

[zy041225]

There are still not enough region that I want. Many SNPs cannot be located in the data. Besides, if there are more than one SNPs in a same region, do you think their centiMorgans are the same?

Answer 1

[Giovanni M Dall'Olio]

A quick and dirty solution is to do a linear interpolation:

R 
> interpolated_map = approx(x=hapmap_snp_positions, y=hapmap_snp_cM, xout=yourdataset_snp_positions)

[Mr Locuace]

One problem with this interpolation method is that when there are gaps of several SNPs, some of them get the same genetic distance (cM).