I just came cross to paper published in nature genetics , "Including known covariates can reduce power to detect genetic effect in case control studies". http://www.ncbi.nlm.nih.gov/pubmed/22820511
I am not expert in statistics so I am not able to fully grab the results from this paper. I use to think that if there is some relationship among primary phenotype and the covariate and suspected relation between SNP and covariate then it should be included in the model. It would be great if some one can clarify the use of covariate in simple biological terms.