I want to use my PLINK files for gcta but get the following error message:
Error: Duplicate SNP name found: "AX-83382164"
The snp ids in our file correspond to codes provided to us by Affymetrix. The AX code here is the first snp ID in our file (there are no duplicates). Am I getting this error because GCTA does not recognize these codes (i.e. it expects rs numbers)? Is there a different reason?