Hello ! I would like to use two different datasets for genotype imoputation : 1/ 1000G data 2/ Simons foundation project data

I tried to combine both data sets but there are many different reference allels between both data sets. Could you suggest any easy way to combine them ? If not, I am using Impute5 for the imputation and it doesn't accept more than 1 refernce data set , is there any other program accepting 2 data sets other than Impute2 ( bcz it's slow and old ... )

Thank you very much !