There are many posts on the web regarding QC steps pre and post-imputation.
Does applying below (new?) 10% MAF difference rule make sense, pitfalls?
Here is the process:
- Get MAF for imputed set, using SNPTEST with flag
- Convert imputed set to hard-calls using gtools with flag
- If the MAF from step 1 and step 2 differs more than 10% than exclude the variant.
- GWAS is 50K vs 50K case control samples.
- This step is applied after
info > 0.4filter.