Dose PSEQ calculate HWE based on controls in the association analysis?

Question

[Randel]

I am using the v-assoc command in PSEQ to do the association analysis. Just to make sure, is HWE (Hardy-Weinberg disequilibrium test p-value) there calculated based on just controls or all samples? Thanks a lot for any hint!

https://atgu.mgh.harvard.edu/plinkseq/assoc.shtml

Answer 1

[Randel]

After tested with an example, I learned that PSEQ uses all samples (both cases and controls) to calculate the HWE.

Then there is another question, is it more accurate to calculate HWE just based on controls, given cases will deviate from H-W for sure?