mismatch allele problem PLINK

Question

[luca.sclisizzo]

Hello,

I'm training to perform GWAS with PLINK. I'm trying to do the PCA with this script 1. When I run it the console tells me

Warning: 648750 --score file entries were skipped due to mismatching allele codes. Error: No valid variants in --score file. 

I can't understand where is the issue. Do you have any ideas?

Thank you,
Luca