Question

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

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11.5 years ago

zy041225 ▴ 70

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 • 14k views

ADD COMMENT • link updated 11.4 years ago by Giovanni M Dall'Olio 28k • written 11.5 years ago by zy041225 ▴ 70

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How to convert centimorgan to base pair

ADD REPLY • link 11.5 years ago by Pierre Lindenbaum 164k

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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?

ADD REPLY • link 11.5 years ago by zy041225 ▴ 70

score 5 · Answer 1 · 2013-07-04

5

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11.4 years ago

Giovanni M Dall'Olio 28k

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)

ADD COMMENT • link 11.4 years ago by Giovanni M Dall'Olio 28k

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

ADD REPLY • link 8.8 years ago by Mr Locuace ▴ 180