When doing triangulation, I can end up with a segment shared among 3 in a GEDmatch compare where I have the cM for each pair of the three, but not the cM for the overlapping portion of the segment. I was unable to find a calculator where I could input the chromosome number and the beginning and ending position numbers. For example, I'd like to know the cM for a segment from 217,656,670 to 227,193,370 on Chromosome 1.
There is a service to turn a physical chromosome position (measured in base pairs, "bp") into a linkage position (measured in centiMorgans, "cM") here:
To get the cM for a segment given its begin and end positions, you would use the web site to convert each of the two positions into linkage positions and then subtract the start linkage from the end linkage.
For your chromosome 1 segment from 217,656,670 to 227,193,370 you should get linkage position from 231.07 cM to 237.65 cM. The length is then (237.65 - 231.07) = 6.6 cM.
Notes on using the Rutgers site: You should put one position per line into the input box, and use only digits, e.g. just "217656670". You choose the build (probably 36) and the chromosome number from the dropdown lists. Under "Query Header" choose "Absent". On the results page, you probably want to use the value from the "Sex-averaged (Kos cM)" column. Males and females have quite different linkage values, but genealogical segments are generally characterized by the average of the two values.
Hendrik Wendland has created a free tool for Windows (donations accepted) called MapS Converter that you can download. It can calculate genetic distances and convert between Build 36 and 37. It is available at Hendrik's MapS Phasing site: www.maps-phasing.com
For example, in the screenshot, I entered the Base Pair addresses you gave as an example in your question into the Build 36 values, I then press the two arrows at the bottom right. It then calculates the Build 37 values and the genetic distance of 6.58 cM.
The value is sex-averaged. By selecting two women or two men at the bottom, you will get female and male values.
Alternatively, you can enter Build 37 numbers (if your numbers are from 23andMe or Living DNA) and get Build 36 equivalents. Or you can enter a start location with a cM value and it will return the end location.
It is a nice little tool, well designed, and easy to use.
I didn't see such type of calculator. But I can imagine the next algorithm:
- As we know each chromosome has it's own value for number of base pairs and cM. Also there is no direct connection between bp and cM, because bp is physical number of pairs and cM is the measure of recombination probability (or rate). Please note that we don't know HOW MUCH base pairs are precisely in your chromosomes, but the human reference genome will give us enough precision despite it can differ from yours particular.
- So we can can took table data for whole length choromosome in bp and cM. The table data can be taken from here. Also wikipedia has info about number of bp in each chromosome.
- And then use linear approximation:
your_cM = (whole_chr_cM) / (whole_chr_bp) * (end_bp - start_bp)