Problem with merging 2 Dataset on plink

Question

[Leonida Monaco]

Hi there . I have a problem with merging two file sets with PLINK.

94 SNPs have different physical position, even if I already check about the Nomenclature. Both file sets came from hg19. But I have noticed how about 100.000 SNPs have different allele codes between the two file sets. And it is not a Flip Strand problem. I have in one data set, take this as an example but there are more, a SNP in one file sets with A/G in the other C/A.

Is there any that can help me to solve this problem?

Thanks a lot