This repository contains the software implementation of QTLEnrich (v2), a tool that assesses enrichment of common variant associations for a given complex disease or trait among molecular quantitative trait loci (QTLs), such as expression QTLs (eQTLs) and splicing QTLs (sQTLs) in a given tissue, correcting for potential confounding factors (MAF, distance to TSS, local LD).
QTLEnrich (v2) is an extension of eQTLEnrich published in Gamazon, Segre, van de Bunt*, et al., Nature Genetics (2018), 50(7):956-967, that accounts for increased discovery power of eQTLs in GTEx release v8 (Genome build hg38) and additional QTL types. The updated version of QTLEnrich is described in the GTEx v8 main paper: GTEx consortium, BioRxiv 2019 (provisionally accepted at Science 2020), where we applied QTLEnrich to GWAS of 87 complex diseases and traits and eQTLs and sQTLs in 49 tissues. A methods paper is also under preparation.
Authors: Andrew Hamel, John Rouhana, written in the Segre lab under the guidance of Ayellet Segre, Massachusetts Eye and Ear, Harvard Medical School, Boston, MA
For questions or comments regarding this tool, please contact Andrew Hamel at andrew_hamel at meei dot harvard dot edu, and Ayellet Segre at ayellet_segre at meei dot harvard dot edu.
Date: January 8, 2020
src: the directory contains scripts for the software pipeline and for plotting with relevant instructions
data: the directory contains input files required to run QTLEnrich for GTEx v8 QTLs
examples: sample data for running QTLEnrich on a given trait and tissue pair
QTLEnrich was written in Python (at least 3.6) and R (at least 3.6.1) and requires the following libraries and modules:
Step by step description for running QTLEnrich, preprocessing of input files, and plotting can be found in src/README.md. Instructions are centered on using GTEx v8 data, but can be applied to any non-GTEx QTL datasets.
The QTLEnrich software is distributed under the terms of the BSD 3-Clause License. See LICENSE.txt file for more details.
GTEx Consortium, "The GTEx Consortium atlas of genetic regulatory effects across human tissues", BioRxiv 2019 (accepted at Science 2020) (https://www.biorxiv.org/content/10.1101/787903v1)
Methods preprint in preparation, coming soon!
Last updated: May 26, 2020