We recommend first regressing covariants out from the original phenotypes, and then provide bfGWAS the corrected phenotypes (i.e., residuals from the regression model with covariates).
It is unclear to me what this means and how to go about determining the corrected phenotypes. Typically, in an association test with covariates, a regression would be performed using a model like
pheno ~ snp + covariate
I could then get the residuals from this model. However, I'm not certain how to go about it for all SNPs, and then adjust the phenotypes. I have case-control data, so the phenotypes are binary.