How to combine two Genome-wide Association Study (GWAS)? I did a GWAS analysis in the past for antibiotic resistance of E. Coli and the results were interesting (matching the literature). I did a new GWAS analysis for some new samples, but the results are not in agreement with the previous GWAS and the literature. So, I was wondering if the combination of them would be in agreement with the literature, as having more samples to support an argument is always a good idea.

So, my question is how I can combine two GWAS study and what quality control steps do I need to follow?
The first way is to combine two samples and re-run GWAS. A second way is to do a meta-analysis using GWAS results.