Bharati got the most, I would think using SHAPEIT to do the phasing and IMPUTE2 to do the imputation is the easiest. IMPUTE2 webiste will be a good starting point. In fact, quality control before imputation is more important, because bad input gives worse output.

Thanks Dr. Bharati and Dr. Xu. According to your suggestion, I used IMPUTE2 software for final imputation. Also used 50 chunk and got 50 .impute2 file for every chr.

Moreover I converted the files with the probabilities for the three genotypes into dosages file.

Now, how can I convert those .impute2 or .dosage files to plink format .bed files?

Hi, sorry, I've been in holiday for a while.

You can use Gtool.

http://www.well.ox.ac.uk/~cfreeman/software/gwas/gtool.html