I'm trying to compare two vcf files, and I understand that VCFtools output will definitely show vcf1 and vcf2 differ, when they are AA vs TT. But how about the following two cases:
1. AA vs AT -- When I see ALT1 column is A, ALT2 column is T, how would I know it is AA vs TT, or AA vs AT?
2. What if AT vs AC?
Thank you very much.