Hello!

I've been trying to merge my own data with 1000genome data to calculate PCA. What I've done so far is: 1) Extracted SNPs from 1000genome that match with my data 2) Merged the two files 3) Used --flip for variants that gave a warning 4) Merged the two files again 5) Removed variants that were still problematic.

Once I did all of this, the genotyping rate for the final merge were 0.92. When I checked the problem, the 1000g data ends up having around 0.1 missingness, so even if I use --mind to increase the genotyping rate, it removes all of these individuals.

I'm still new to this, so I would appreciate any advice on if this is normal, or what could I do to fix it?

Which 1000G data are you using? It should be fully haplotype resolved (imputed + phased) and have no missingness.