The computation of IQS requires the posterior probabilities of AA, AB and BB as output by the imputation program. For one SNP genotyped on N individuals, the probabilities can be readily tabulated into a 3×3 table where each cell, nij, represents the number of individuals with true genotype i and imputed genotype j (Table 1). Note, in this scenario, nij may not be an integer due to imputation probabilities being reported rather than imputed genotypes.
