Hi there. I have used PGDSpider to convert a plink ped file to a Bayescan format file. The map file is specified in the associated spid file for the conversion.
However there seems to be no way to relate the index in column 1 back to the loci in the map/ped file? when doing the Bayescan analysis I can see there are outliers, but i don't know what loci they are.
There are 100982 loci in my plink files and 100984 index in the bayescan file. I have reran the analysis and even tried breaking it into different chromosomes but there is always 2 more index than loci. Does anyone have any experience of this or can anyone explain this to me? Thank you for your time