Hello,

I currently have a dataset consisting of approximately 500 disease cases with exome sequencing data. I understand hardy-weinberg filters are typically applied to controls, but was wondering if conducing quality control on a case population would alter the stringency of the filter.

I am currently using a filter of P < 0.05 to be conservative. The p-values are generated via a chi-squared test using vcftools --hardy.

Any insight on this matter would be greatly appreciated!

Thank you.