Evidence for departure from HWE has been userd in many applications of discrete P-values in HWE testing.

Wallace, B., 1958 The comparison of observed and calculated zygotic distributions. Evolution 12: 113–115. plink2 --bfile ft_pedigree --freq alt1bins=0.01,0.02,0.03,0.04,0.05,0.1,0.2,0.3,0.4,0.5,0.6,0.7,0.8,0.9,1 keep-fewhet : When significant population stratification is present, this test can be expected to fail in the too-few-hets direction on some normal variants. When using --hwe for quality control, you probably want to keep these variants. plink2 --bfile ft_ped --indep 1000 100 2 # window size, step, the VIF(variance inflation factor) threshold: 1/(1-R plink2 --bfile ft_ped --indep-pairwise 1500kb 1 0.7 # if the window size unit is kb, the step is set to be 1.Zou, G. Y., and A. Donner, 2006 The merits of testing Hardy-Weinberg equilibrium in the analysis of unmatched case-control data: Eighty Years Ago: The Beginnings of Population Genetics, James F. Crow and William F. Dove, Genetics 119:473–476, 1988. Cohen, J. E., M. Lynch and C. E. Taylor, 1991 Forensic DNA tests and Hardy-Weinberg equilibrium. Science 253: 1037–1038. Gomes, I., A. Collins, C. Lonjou, N. S. Thomas, J. Wilkinson et al., 1999 Hardy-Weinberg quality control. Ann. Hum. Genet. 63: Welcome A/Z Plan Participant Now you can view exclusive price savings on our Build & Price shopping tool.

Weir, B. S., 1992 Population genetics in the forensic DNA debate. Proc. Natl. Acad. Sci. USA 89: 11654–11659. A Note on Exact Tests of Hardy-Weinberg Equilibrium, Janis E. Wigginton, David J. Cutler and Gonc¸alo R. Abecasis, Am. J. Hum. Genet. 76:887–883, 2005.