I’m pretty new to statistical genetics, and I’m wondering whether Hail’s linear regression outputs separate beta values for additivity/dominance.
When I learned about GWAS, I was taught to define random variables (X_a, X_d) = (-1, -1), (0, 1), and (1, -1) corresponding to genotypes homozygous ref, heterozygous, and homozygous alt, respectively. This would then give you two betas, beta_a and beta_d, whose values tell you whether the trait is additive, dominant, neither, or some mixture.
My guess from the documentation is that it only outputs a single beta corresponding to the genotype (I’m running it the same way as in the documentation—feeding in GT.num_alt_alleles()).
If this is the case, could Hail’s method miss some associations because a trait isn’t strictly linear?