Hi, I have a multiple quaddRAD seq samples for my group of interest, which I have mapped to the reference then processed with Stacks ref_map.pl, got vcf, build tree and so on. The problem is that I need an outgroup and I don't have the quaddRAD seq for it, so I found the genome and WGS data in NCBI for the sample which is suitable for me as an outgroup. What is the best/simplest way to get vcf from both quaddRAD seq and WGS data together? I've found that it's not possible to just merge two vcfs (one from wgs data mapped to my reference, and the other for RAD seq) because the Stacks doesn't make the normal vcf for RAD seq samples (in the ref letter column (4th column) it puts the most frequent base, but not the actual reference base). Obviously, I can just recall vcf for all samples using bcf call, but I wonder if it is normal to process data without Stacks, which is what everyone uses.