p-value threshold for HWE deviation

[blueskypie]

Your paper suggests the following:

For binary traits we suggest to exclude: HWE p value <1e −10 in cases and <1e−6 in controls. Less strict case threshold avoids discarding disease‐associated SNPs under selection. For quantitative traits, we recommend HWE p value <1e‐6.

May I ask two questions?

1. are those cutoffs for human WGS or WES or whole genome microarray?
2. For quantitative traits, use the same cutoff for both case and control?

[Ray-Saif]

May I add another query in this context? You mention in your paper that a "less strict case threshold avoids discarding disease‐associated SNPs under selection", but the threshold used for the cases (,1e-10) is more strict, not less.