Hello. I have a dataset of cases and a dataset of controls which have been genotyped on different platforms. So, for a particular SNP, it can happen that I have the same allele coding both in cases and in controls; or it can happen that I have in controls the reverse of cases (e.g.: A C in cases and T G or G T in controls).
  I want to merge the files of cases and controls, but the allele coding should be consistent: which procedure can I follow? Please, let me know. Thanks!
One possible workflow is described at http://www.cog-genomics.org/plink/1.9/data#merge3 .