This software allows for QTL mapping using linear models and direct meta-analysis of such data through weighted Z-score analysis.
The eQTLgen RNA-seq based eQTL cookbook can be found on our wiki: https://github.com/molgenis/systemsgenetics/wiki/eQTL-mapping-analysis-cookbook-for-RNA-seq-data
The old documentation can be found here: https://github.com/molgenis/systemsgenetics/blob/master/eqtl-mapping-pipeline/README_old.md