Hardy-Weinberg Equilibrium and MAF filtering post imputation

Hardy-Weinberg Equilibrium and MAF filtering post imputation

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Hi, I have 5 million variants after imputation using Beagle 5.2 after filering low confidence imputation ( DR2 < 0.9). Pre-imputation QC was that I removed rare variants MAF < 0.05 and use only variants with no missing genotype data (–geno 0 / plink1.9), and also Hardy-Weinberg Equilibrium threshold of 10^-6. However, I wonder whether I should do HWE and MAF filtering again after imputation. My guess is that I don’t need to since those results are coming from the “reasonable” original data that I supplied, but I don’t have strong biological background to be honest, so I would appreciate if you can explain it in a beginner friendly way why is it good or bad to do so. Thank you in advance.


QC


beagle


imputation

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