I would like to ultimately create my own set-file to use with Plink to annotate some GWAS data that I have. I don't even know where to begin, what program to use. I have an annotation file from the NCBI, a .fa file. I have a GWAS file in bed/bim/fam binary format. Ultimately I want to make a set file for PLINK set-based tests. Any ideas? Thank you!