How many SNPs could be excluded from the analysis?

Question

[khn]

Hello,

I am merning two datasets from different platforms using plink. I cannot complete merging as I encountered as below.

For example, per bim files,

Dataset1: SNP1: alelles T and G --- This is correct, based on dbSNP

Dataset2: SNP1: alleles GC and G --- This SNP is not triiallelic. GC is wrong.

Dataset1: SNP2: alelles T and A --- This is correct, based on dbSNP

Datase2: SNP2: alleles 0 and AT --- 0 and AT are both wrong.

There are more than 200 SNPs with these kinds of inconsistencies, so I cannot complete merging. If so, even the number of these SNPs are more than 200, can I just exclude those SNP and complete merging?

Thank you in advance!