What is the best QC to do on imputed UK Biobank data?
I am receiving imputed data from UK Biobank to conduct a GWAS on. Previously I have carried out GWAS on genotype data, which I have QC’d for missingness per individual and per SNP, sex discrepancy, MAF filter < 0.05, heterozygosity rate, cryptic relatedness and population stratification.
However, from reading several papers about QC of imputed data, I do not carry out any of these QC checks on the imputed data. What QC procedures should I expect to carry out on UKBB data? Just to filter by info score?
Or would it be better to carry out the initial QC checks on the genotype data and then impute myself?
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