Dear experts, I have a genotype data which I want to use for GWAS. The genotype data contains all columns, except allele columns i.e. Ref and Alt alleles. It has all other information, such as chromosome position, chromosome number, and the alleles in my sample etc. It has already been aligned to the reference genome, but I am confused about the Ref and Alt alleles. Is there any way to get it? any software which can extract reference and alternative allele? It is not in any format. Its just a text file. I need to find the alleles for association.