How to choose --hwe threshold?
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.
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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.
I'm looking at ICD10 codes, so binary traits.