We illustrate the use of Bayes factors for examination of HWE in GWAS. In this context, testing for HWE is used as a method for carrying out quality control, and in particular to detect SNP specific genotyping errors. Fisher's exact test is the recommended frequentist procedure (Wigginton et al., 2005; Balding, 2006), but there are a number of difficulties in implementation. In a multiple testing situation one must select a criterion to control in order to specify a significance threshold, and by far the most common approach is a Bonferroni correction. However, the rationale for control of the family-wise error rate (FWER) is not obvious in a genome-wide quality context when one would not expect all nulls to be true. Even if one accepts that this is the correct quantity to control, the choice of a specific threshold is difficult. There is no agreed threshold in the literature, as Wittke-Thompson, Pluzhnikov, and Cox (2005, p. 967) state, “. . . there is little consensus on the correct thresholds for identifying DHW (departure from HWE) in the context of large-scale studies”
