In S.A.G.E. what is the difference between a phenotype and a trait?
A phenotype is a general term that does not specify how the program is to use the variable. A trait is a phenotype that is designated to have a primary role in analyses. Any phenotype, trait or covariate may be used as a trait or covariate in any analysis. However, when defaults are used, only the phenotypes designated as traits are automatically used as traits in the analysis. This distinction is for user convenience, so that it is not always necessary to specify which phenotypes are to be analyzed.