Parameters | Genetics | Perform association tests on selected markers

Perform association tests on selected markers
Check this box to perform association tests (Genotype and/or Trend) on selected markers.
Note: When the model includes random effects (the K matrix), the multi-marker model selection method selects variables from the rotated data. Therefore, Genotype and/or Trend tests are not feasible. However, checking the Perform association tests on unselected markers conditional on selected markers check box, and thereby fitting the selected variables on the unrotated data, makes the Genotype and/or Trend tests feasible1.
To Specify This Option:

Rakitsch, B., Lippert, C., Stegle, O., and Borgwardt, K. (2013) Lasso multi-marker mixed model for association mapping with population structure correction. Genetics 29(2): 206-214.