I am currently having trouble to convert a .vcf file to a bayescan input that takes into account the population information. I have a dataset of 34 individuals divided into 10 populations and over 34K SNPs to analyze. I have tried converting a .vcf file (generated through the STACKS program) to a bayescan input file using PDGspider. Unfortunately, while the conversion is successful, PDGspider seems to ignore the population information I have provided in the SPID file (e.g. a simple text file containing two columns, one with individual information and another with population information). The conversion generates a file considering a single population only, and - apparently - does not distinguish individual information.
I am assuming I have the wrong idea about how to make a population info file or I could be missing some necessary steps in between the VCF -> Bayescan conversion. I have seen other posts here and elsewhere ( I do not remember if it was on ResearchGate or google groups) suggesting A three-step conversion, like VCF -> PGD -> bayescan, but it did not work for me.
Any thoughts? Help would be greatly appreciated!
Very best, Leonardo.