VCFtools: how does --diff option consider genotypes

Question

[DVA]

Hello,

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.

Answer 1

[DVA]

Well upon a few testing, I found that VCFtools does not distinguish the above two situations. I think it is sometimes better to just write a simple code to process two vcf comparisons.