Motivation:Despite recent advances of modern GWAS methods, it is still remains an important problem of addressing calculation an effect size and corresponding p-value for the whole gene rather than for single variant. Results:We developed an R package rqt, which offers gene-level GWAS meta-analysis. The package can be easily included into bioinformatics pipeline or used stand-alone. We applied this tool to the analysis of Alzheimer's disease data from three datasets CHS, FHS and LOADFS. Test results from meta-analysis of three Alzheimer studies show its applicability for association testing. Availability and implementation:The package rqt is freely available under the following link: https://github.com/izhbannikov/rqt. Contact:ilya.zhbannikov@duke.edu. Supplementary information:Supplementary data are available at Bioinformatics online.