How To Calculate The Genomic Inflation Factor From The Plink Output?

Question

[Liyf]

Hi, I have a question about genomic inflation factor(GIF).

When I use plink to do logistic association, I noticed that some SNP have NA in P, the question is when I calculate the GIF,do I need to remove these snp or set NA to 1?

Thanks!

Answer 1

[Maxime Lamontagne]

Actually, when you are using plink to make association test, the genomic inflation factor is calculated and can be found at the bottom of the log file. If you have NA in your output, check those SNPs. Maybe their frequency is 0 or they are monomorphic.

Answer 2

[Liyf]

Yes. If you use --asso there will be GIF. But if you use --logistic there will be non.