Coding genotype for diploids

[YannDussert]

Hi,

I would be interested in testing treeWAS in a clonal diploid organism. Is it possible, and if it is, how should I code genotypes?

Maybe more clearly, for each given site, I have three possible genotypes: 0/0, 0/1, 1/1, with 0 the reference allele and 1 the alternate allele. Should I use three columns per site (one for each genotype) or two columns (one for each chromosome)?

Thank you in advance for your answer.

Best regards,
Yann