Now that I have my basic GWAS workflow sorted out I was looking more into the LinearMixedModel functionality. I know the documentation mentions this functionality is experimental.
I was wondering if other users have gotten a LinearMixedModel to work, and if not, if this is something dev’s are looking into? Would be great to have functionality so I can more directly compare to Bolt-LMM, say if a collaborator is using LMM and we want to do a meta-analysis!
Right now I try running:
lmm, _ = hl.linear_mixed_model( y=mt.pheno.trait, x=[1.0, mt.pheno.cov1, mt.pheno.cov2, mt.pheno.cov3], z_t=mt.GT.n_alt_alleles(), p_path=bucket+p_fname)
which just seems to keep running without an end in sight. Have tried running it for 4+ hours.
Any tips? Or is this functionality not a current priority in Hail’s feature set?