heroico / integrative

Software Pipeline for Integrative Genetic Association Analysis: Probabilistic Assessment of Enrichment and Colocalization

ENLOC: Enrichment Estimation Aided Colocalization Analysis

This repository contains the software implementation of enloc, which enables integrative genetic association analysis of molecular QTL data and GWAS data. The statistical model and the key computational procedures are described in this manuscript.

For questions/comments regarding to the software package, please contact Xiaoquan Wen (xwen at umich dot edu).

License

Software distributed under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. See LICENSE for more details.

Repository structure

• src: the directory contains scripts for the software pipeline and relevant instructions
• examples: sample data and a step-by-step guide for reproducing the analysis described in the manuscript

Dependency

The software pipeline assumes the availability of the following executables

• perl
• torus
• dap
• openmp_wrapper

Molecular QTL data analysis

Enloc also requires specific (Bayesian) analysis of molecular QTL data, which can be achieved by the dap and torus. A detailed step-by-step guideline with real data is provided.

Citation

• Wen, X., Pique-Regi, R., Luca, F. Integrating Molecular QTL Data into Genome-wide Genetic Association Analysis: Probabilistic Assessment of Enrichment and Colocalization. PLOS Genetics. 2017 Mar 13(3): e1006646.