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Bayescan file format. how to relate index back to loci after conversion from plink ped file

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

bayescan pgdspider plink population genetics
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written by s0782801 • s0782801

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