I have a VCF from which I got the .ped and .map files using plink. However, the genetic distance (3rd column) has been set to 0. I want the map file to include the genetic distances. For my analysis, I am assuming a constant recombination rate of 15 kb/Cm.
Does plink have a command where you can provide the recombination rate so the output map file has the genetic distances? I was not able to find how the calculation is done from their manual.
I have thought about calculating them manually, but I am slightly confused with the formula -
If I have a VCF file having the following SNPs...
Chrom_01_v3 613 Chrom_01_v3 714 Chrom_01_v3 779
is it 714/15k or (714 - 613)/15k? In the latter case, since I have SNPs that are quite close to one another, I am getting genetic distances that are too small for my analysis.
My goal is to do IBD through the R package isoRelate which requires the input as .ped and .map format. My end goal is to get a Manhattan Plot.