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

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!

distance
• 14,555 views • link
updated by Giovanni M Dall'Olio Giovanni M Dall'Olio • written by zy041225 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?

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written by zy041225 zy041225

1 answer

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)
• 774 views • link
written by Giovanni M Dall'Olio Giovanni M Dall'Olio

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

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written by Mr Locuace Mr Locuace

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