I am doing Genome-Wide Association Study data analysis. So far, before imputaion, QC analysis, association analysis, Imputation went well (of course with great efforts). But, after imputation I am quiet like confused, as I have done my imputation with Impute2. I have converted files from Impute2 output to PLINK output and also done dosage analysis.
But with literature survey, I am getting confused whether or not I can use PLINK for post-Imputation data. As, most of the papers are mentioning SNPTEST is meant for data analysis after imputation with Impute2. And I did it too, but if I see output of SNPTEST, I am hardly getting anything from it's output. Eventually leads, as per me, to stick with PLINK.
So my specific question is, shall I stick with PLINK analysis for Impute2 imputed data? If not, how to interpret SNPTEST output, especially Bayesian statistics output?