The Filter to Select Null SNPs field is an optional parameter that you to select marker variables to use as null SNPs, which are used for the calculation of principal components for individuals. Only markers that meet the condition(s) specified will be used to compute principal components for individuals.
When performing a genome-wide association study, you do not need to specify null SNPs, but for smaller sets of SNPs, it is recommended that SNPs known not to be associated with the trait be used as null SNPs. By default, all marker variables are used in the PCA.
All Marker Variables (including Null SNPs) are still included in the analysis for association with Trait Variables. It is necessary to use quotes when filtering data using values of a character variable (e.g, Chromosome = "X") but no quotes are required for filtering by values of a numeric variable (for example, ProbChiSq < 3). The variable names used in this statement (for example, Chromosome, Position) must exactly match those in the Annotation SAS Data Set.
Note: You must specify all variables that correspond to the markers in the entire annotation data set as Marker Variables.