Check this box to treat multiallelic markers as multiallelic in the analysis instead of converting them to biallelic markers in terms of the non-major alleles.
When this option is checked, the Expand Multiallelic Genotypes process is run and genotypes are converted to expanded representations with one column per allele (with the last allele dropped). The expanded genotypes are used for calculating the Q and K matrices. The Marker-Trait Association process is used to run the Q-K analysis to accommodate the multiple alleles per marker in a single model.