I have merged VCF files of every individuals of a particular population using VCF merge. But I am not sure which SNP is coming from which individual. I tried to convert the merged VCF file in PGDSpider to generate GENEPOP format data to use in Lositan for Outlier detection. However, Lositan only detects one population. What could be the best way to merge different VCF files for different populations into one Genepop file to use in Lositan for Outlier detection?
Thank you in advance,