I have two plink binary files - one containing only polimorphic sites (400k snps), the other one - plink file with reference data containing more sites (500K). How to merge them, so that those extra 100K snps will not be assigned to missing in a merged file?
I have tried first to devide my 400K binary file into the one with genuine missing sites and another - with the rest of the sites. Merged missing sites separately, but not sure how to proceed with the rest of the sites. Was thinking about changing the format to tped/tfam, but then I lose the reference info in order to go back to a proper bim file with alelle info.
Thank you!