Hello, I am using the output vcf from tassel uneak as the input vcf for pgdspider. Then I am trying to use pgd spider to convert the file to genepop for lositan to find outlier snps. In pgd spider I am inputting a population definitions file like:
Fe-36 TW_1 Fe-51 TW_1 Fe-76 TW_1
there are 4 populations: TW_1, 2, 3, ad 4. But when I load the file into lositan, it is only recognizing one population.
are there any oversights on my part that could result in that conversion error?