find position of snps in cM, given recombination map from ldhelmet
Entering edit mode
3.6 years ago
Jautis ▴ 510

Hello, I have a recombination map calculated from LDhelmet which has estimates of recombination rates for windows of the genome (in recombination events per generation per bp) and a separate file of SNP locations which I would like to transform from base number to location in centiMorgans. Is there an easy way to do this computationally? The best strategy I've been able to devise is, for each site, taking the sum of previous windows and then the proportion of the current window. However, that seems very inefficient when given hundreds of thousands of SNPs. Any suggestions for a way to calculate this (or program out there) that would be more efficient?

##Recombination rate data
 start     end      rate/bp     length 
 101       400      0.004       300
 401       900      0.0001      500

## SNPs
base pair

# So for this SNP, the position would be 300*0.004 + (400/500)*0.0001
recombination genome physical position • 935 views

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