Protocol to merge cases and controls

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!

ADD COMMENT • link updated 7.3 years ago by chrchang523 11k • written 7.3 years ago by alessandrotestori7 ▴ 420

which have been genotyped differently.

Please be as informative as possible when asking questions.

Thanks, it is very helpful. After the merge fails because alleles are not consistent in cases and controls, I flip alleles in the .missnp file which is generated, thus obtaining new binary files. With these files and the cases I do the merging; the alleles in the .bim files of cases and controls are almost always the same, except for very few cases in which allele1 and allele2 columns are inverted (e.g.: A G in cases and G A in controls). However I can now manage to merge files without problems, so I guess that is not a problem. I am though wondering whether it is fair to have these alleles inverted in cases and controls. Is it a matter of different frequencies?

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