I'm trying to convert my VCF file to Bayenv2 format with PGDSpider 188.8.131.52. My problem is that it recognises a lot of SNPs as non-polymorphic (although they actually are...). I've realised that some of my SNPs have in the VCF REF column more than just one alelle (I guess they are insertions) and it's only those SNPs the ones that PGDSpider recognises as polymorphic.
I don't know if someone is facing the same problem, but I'd be glad to discuss what can be done, because I'd like to keep all those SNPs in my analysis. Thank you very much in advanced!