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Background  Increasing number of eQTL (Expression Quantitative Trait Loci) datasets facilitate genetics and systems biology research. Meta-analysis tools are in need to jointly analyze datasets of same or similar issue types to improve statistical power especially in trans-eQTL mapping. Meta-analysis framework is also necessary for ChrX eQTL discovery.    Results  We developed a novel tool,   meta-eqtl  , for fast eQTL meta-analysis of arbitrary sample size and arbitrary number of datasets. Further, this tool accommodates versatile modeling, eg. non-parametric model and mixed effect models. In addition,   meta-eqtl   readily handles calculation of chrX eQTLs.    Conclusions  We demonstrated and validated   meta-eqtl   as fast and comprehensive tool to meta-analyze multiple datasets and ChrX eQTL discovery.   Meta-eqtl   is a set of command line utilities written in R, with some computationally intensive parts written in C. The software runs on Linux platforms and is designed to intelligently adapt to high performance computing (HPC) cluster. We applied the novel tool to liver and adipose tissue data, and revealed eSNPs underlying diabetes GWAS loci.

Meta-eQTL: a tool set for flexible eQTL meta-analysis