How to choose --hwe threshold?

Question

[_quantum_girl_]

I want to analyze a series of rare (MAF<0.01) co-mutations. For doing the QC I'm setting --geno 0.1 and --hwe 1x10^-15. How should I choose these threshold though? My data consists of approximately 300k individuals and 500k variants.

[bk11]

What type of trait (binary or quantitative) are you studying in these data? You should use different HWE p value thresholds for cases and controls in binary traits. And use different HWE p value criteria for quantitative trait. You can use this article as a reference.

[_quantum_girl_]

I'm looking at ICD10 codes, so binary traits.