Hi everybody !
It's a simple question, but I can't find any information on that either on the Internet or in the PDF manual for PGDSpider. I'm trying to convert a VCF file into a Bayscan input file with PGD spider. The .VCF file obtained with SAMTOOLS contains the SNP information on 24 individuals : 12 in a population and 12 in another population. When I edit the SPID file in PGDSpider just before launching the conversion task, I'm asked if I want to include a file with "population definitions". Then, I have to select an input file that contains these population definitions. Since I want a Baysecan input file, I need this population information : the Bayescan file is supposed to contain information on the SNP count PER POPULATION. The problem is that I don't know what this population definitions file is supposed to look like and there is no example in the "example" folder given with the program. PGDSpider has to know which samples in the VCF file are in which population.
I have tried several input formats, but they all got rejected. Can somebody help me ? I thought of writing a python script to parse the VCF file and create the bayescan input file myself, but it would be a lot faster and easier to use PGDSpider.
Thanks for any help ! I appreciate,