I am trying to merge two different PLINK files genotyped on the same platform. However, I found some inconsistencies that could not be solved by the
--flip command. I checked the SNPs that could not be merged after the flip and found this type of problem:
4 rs10000432 68.93 47511781 T C
4 rs10000432 68.93 47511781 A C
One of the alleles is different, while the other allele is the same on both files.
What should I do on this case? I wasn't expecting to find these type of issues on these datasets since both were genotyped on the same platform.