Question: Convert Snp Physical Position(Bp) Into Genetic Distance(Cm)
3
gravatar for zy041225
5.8 years ago by
zy04122560
China
zy04122560 wrote:

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 • 8.3k views
ADD COMMENTlink modified 5.6 years ago by Giovanni M Dall'Olio26k • written 5.8 years ago by zy04122560

related:

Position of genes in centiMorgans?

How to convert centimorgan to base pair

ADD REPLYlink written 5.8 years ago by Pierre Lindenbaum116k

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 REPLYlink written 5.8 years ago by zy04122560
4
gravatar for Giovanni M Dall'Olio
5.6 years ago by
London, UK
Giovanni M Dall'Olio26k wrote:

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 COMMENTlink written 5.6 years ago by Giovanni M Dall'Olio26k

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 REPLYlink written 3.0 years ago by Mr Locuace90
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