I meta-analyzed the results of 2 genome-wide association studies using PLINK.
plink --meta-analysis file1 file2 + logscale qt --out results
I created a Q-Q plot with the resulting p-values. The p-values look to be inflated. I am unsure whether this is resulting from inadequate control for population substructure or if it is due to the polygenicity of the phenotype. I would like to know the value of the genomic inflation factor lambda (which was calculated using PLINK with the --adjust flag in the original GWAS - neither used in the meta-analysis were inflated).
Is there a way to have PLINK calculate the genomic inflation factor lambda and output it in the log file for a meta-analysis of multiple GWAS in the same that it can be done for a single GWAS?
Any input or suggestions would be appreciated.