I have 2 datasets and want to analysis the XPEHH scores by selscan.
I used plink and beagle to pre-process my datasets.
When I try to run the selscan. my datasets have same haplotypes but not the same loci in my map file? I dont understand why my map file can not work in selscan. Do you have any ideals for this?
How to generate the map file for selscan?