My project goal is to compare the variants between populations. I have 8 RNA seq libraries that I have mapped to an unannotated reference, and called variants with Lo-Freq. I am wondering how I can use these VCF files to run a meaningful analysis/comparison of the variants between the populations.
have you in mind any population genomic parameter for analyzing the genomic diversity? Probably plink is the tool that you need. It allows us to compute the principal components analysis for identifying the population structure. It also allows you to perform an association analysis between the two populations (previously you would need to merge the files of each population).