I use eigenstrat to correct population structure in my multiple GWAS. I want to calculate the genomic inflation factor before correction, I think GIF should be large, for population structure, but my GIF is too large, is 2.14! I never see so large GIF, even before correction, I do not know this may be something wrong with my work?
A large GIF may mean you have made a calculation error, or it may mean you have a P value distribution that doesn't fit the normal GWA model for some reason. It could be correctly indicating that your data violate the population sub-structure assumptions normally made for a GWAS. If you "think the GIF should be large", then what makes you think that 2.14 is "too large"? I think substructure is only one form of bias that could cause a large GIF, though my understanding is it's the most typical cause. If you do a PCA on your genotypes, is there obvious structure, and can you relate that back to ethnicity or region?
You don't tend to see large GIF values in publications because a large GIF indicates there's something about the data that needs to be transformed or filtered before you can do the GWA analysis.