I have some SNPs data and I want to convert the SNPs physical position in base pairs to their genetic position in centiMorgan. I will appreciate you contributions. Thank you.
Check this post and you will get an answer:
https://www.researchgate.net/post/How_does_to_convert_physical_distance_bp_for_instance_maize_RefGenV1_to_Genetic_Distance_in_maize_cMNAM_map2
The genetic positions are based on random recombination frequency of marker alleles in a given population segregating for the locus. Hence, one need a mapping population to calculate the genetic distance in cM. Therefore, in principle there is no direct way to convert a physical map to a genetic map. In case if you want to guess an relative distance comparision, it is also highly variable across the genome. Usually at at the recombination hot spots around 200-300 Kb can show 1% recombination (1cM), but it can be highly different at other regions of the chromsomes where 1 cM can be around 500 to 1000 kb or more. Can you write it precisely for which purpose you need to convert physical map to genetic map, which may help me to suggest you more.
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