How to calculate Centimorgan lengths from run lengths in one-to-one dna profile comparison

Question

For easier management of a database of dna profiles, I'm creating a tool to perform one-to-one matching on two profiles with snp genotype information.

Basically, something that works similar to GEDMatch's one-to-one matching feature.

Determining the length of runs of half or fully matched snp's, including some allowance for a genotyping error rate, is the easy part.

My question is about converting an snp run length to centimorgans.

I figure that the length needs to be adjusted by the likelihood of a change in the particular region of the chromosome.

Since my dna profiles and the positions of snps are based on Genome Reference Consortium Human Build 37, I figure that his information could be in the reference build, directly or derivable in some way.

Looking at the GRCh37 download files and the definitions of their formats, I'm unable to find such information.

Is this information present in GRCh37, or can it be downloaded from another reference source, and from which field in the dataset can it be retrieved or derived?

Answer 1

Try having a look at this link:

http://bochet.gcc.biostat.washington.edu/beagle/genetic_maps/plink.GRCh37.map.zip

If you unzip the file, there is a file for each chromosome (1:22) and then 3 for the x chromosome. The first column of each file details which chromosome the file corresponds to, the 3rd column gives you the cumulative genetic distance in cM and the 4th column gives you the genomic coordinate (position) in bp.

You can then calculate the distance in cM between two positions from this data by subtracting the cM positions between the two positions you are interested in.