Hello, I am unable to understand that with respect to which allele plink (plink-1.90b3w) calculates the --r/r2. Although, it is written that it is based on the non-reference allele , but when I use major allele in A2 in the bim file, it gives the same matrix as it gives for when A2 is the reference allele.

Does --r/r2 option follow:

0 = both ref allele 1 = one ref and one alt allele 2 = both alt allele

OR

0 = both major allele 1 = one major and one minor allele 2 = both minor allele

OR

something else

I found --keep-allele-order and/or a2-allele do not have any effect on the r/r^2 matrix for a set of SNPs. Is this true or I am doing something wrong?

--ld option is based on haplotype frequency, which is different that --r/r2 option. But my question is the same as above. Which allele they follow (0,1, and 2).

Any help would be highly appreciated. Thank you very much.