Duplicates in plink files (same position, same ref allele but different A1 allele)

Question

[datanerd]

HI all,

I remove duplicate snaps from my files using --list-duplicate vars. However this does not remove the snps with same position , same ref allele but different A1 - one has 0 ).

This creates problem when running shapeit, how do I remove these snaps?

Thanks,
mamta

[Hasanga]

Hi,

I have the same problem as you. Did you manage to find a solution? You'll be kind to share with me if you have.

Thanks !

[Vitis]

Do the SNPs come from normalized VCF, in which multiple alternative alleles have been split into multiple SNP entires? If so, you may be able to fix it by choosing only one alternative allele in VCF then pipe it into plink.