This dataset corresponds to the data and script used for a meta-analysis of genome-wide association studies in tomato for main flavor-related traits. They are based on re-analysis of original data provided in Sauvage et al (2014), Bauchet et al (2017) and Tieman et al (2017). Each file corresponds to one trait containing the following information: SNP, Chromosome (CHR), Position (POS), Reference allele (AL1), Alternative allele (AL2), Betavalue of meta-analysis (BETA), standard error of meta-analysis (SE), Meta-analysis P value(PVALUE), Study direction (Direction), Heterogeneity (HetIsq) and heterogeneity P value (HetPVal). We also provide the script containing the central command lines to perform an imputation-driven meta-analysis. These files contain all the information that are required to perform a further meta-analysis. references Sauvage, C. et al. Plant Physiol. 165, 1120–1132 (2014). Bauchet, G. et al. New Phytol. 215, 624–641 (2017). Tieman, D. et al. Science 355, 391–394 (2017). All SNP positions were provided according to SL2.50 reference genome