PCA analysis of two population

Question

[qstefano]

Hi everyone,

I want to perform PCA analyses to test if my two populations are genetically different or not. I used to do it with PLINK but in this case I have less than 50 samples and 40.000 SNPs. I can't calculate AF with less than 50 samples with PLINK.

Do you know any workaround? Or eventually, a better analysis to test this genetic difference.

Thank you in advice!