# Filtering imputed GWAS SNPs based on a MAF difference of 10%

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:

1. Get MAF for imputed set, using SNPTEST with flag -summary_stats_only
2. Convert imputed set to hard-calls using gtools with flag --threshold 0.9
3. If the MAF from step 1 and step 2 differs more than 10% than exclude the variant.

• This step is applied after info > 0.4 filter.