I'm wanting to calculate a genetic map using ldhat to use as an input for calculating iHS. I've run the interval program and then the stat program on the rates output file to give me a file with the estimated recombination rates between markers (the header line of that file is: Loci Mean_rho Median L95 U95).
From the ldhat manual am I right in believing that those values are the rho/kb between the adjacent markers? If so do I use that value for the input for the iHS or do I then need to multiply it by the distance between the markers?
for example lets say I have 4 SNPs at positions 0kb, 2kb, 3kb, 5kb and an output file that looks like:
Loci mean_rho Median L95 U95
0 100 100 90 110
1 33 33 30 37
2 33 33 30 37
3 34 34 30 36
Would I set the genetic distances for iHS as 0, 33, 66, 100 (cumulative sum of the mean_rho/kb) or would I first multiply by the physical separation to get 0, 66, 99, 167 (cumulative rho)?
