I have been using LDHAT to get recombination maps for a dataset I am currently working on.
I get the output quite fine i.e., all the positions and their respective mean/median rho with 95% CI : LDHAT Output, first column position in kb and second column is rho
However, when using this map with the downstream applications like phasing/imputation the map needs to be such that as the physical positions increase, the genetic positions also increase, such that the tail end of the map has the largest recombination rates & highest genetic position values.
For example, recombination map for chr22 from 1000genomes site 1000 genomes recombination map: rsid, position, genetic position in cM
But the recombinational landscape is not such a skewed distribution, as rates vary based on the chromosomal location etc.
Does anyone know how to convert LDHAT output into a genetic map akin to how 1000 genomes based recombination maps, as used in phasing and imputation within SHAPEIT or IMPUTE2?
Dear Shab86, Have you found the answer?