How to filter info score post-imputation? this is a very basic question, but I cannot find it explicitly stated anywhere: When exactly should I filter the info scores after imputation?

I did imputation in Impute2 and am planning on using SNPtest to analyze, but cannot tell if I should filter the scores in Impute2, SNPtest, Gtool, QCtool, or through python.

I'm hoping to get rid of the poorly imputed results (with an info score cutoff &lt;0.5) in a population of ~4000 (half cases, half controls). After this, I'm running an association analysis -- probably through PLINK, but I'm still figuring out the best way to go from Impute2 to PLINK.

Any help would be greatly appreciated!!
In simple GWAS setups, each SNP is analyzed independently.  In those cases you can filter out SNPs with poor INFO scores at any point.

For analyses that combine information across SNPs (for example FaSTLMM), I would recommend filtering out SNPs before running the step that combines information across SNPs.

So, if you filter right after running Impute2, you should be safe.