geneticresources/pleio

PLEIO

• Pleiotropic Locus Exploration and Interpretation using Optimal test

pleio is a command line tool for performinig meta-analysis of multiple GWAS summary statistics.

Getting Started

In order to download pleio, you should clone this repository via the command

git clone git://github.com/cuelee/pleio.git
cd pleio

In order to run pleio, the following python dependencies must be installed in your system.

• python >= 3.7.4
• pandas >= 1.0.4
• numpy = v.1.16.4
• scipy >= v.1.4.1

To install Python dependencies, you need to install an Anaconda python distribution from LINK. After installing Anaconda, run the following command to create an environment with pleio's dependencies.

conda env create -f environment.yml
conda activate pleio

Once the above has completed, you can run the following command:

./pleio -h

Updating PLEIO

You can update to the newest version of PLEIO using git. First, navigate to your pleio/ directory (e.g., cd pleio), then run

git pull

If PLEIO is up to date, you will see

Already up-to-date.

otherwise, you will see git output similar to

remote: Enumerating objects: 9, done.
remote: Counting objects: 100% (9/9), done.
remote: Compressing objects: 100% (3/3), done.
remote: Total 6 (delta 4), reused 5 (delta 3), pack-reused 0
Unpacking objects: 100% (6/6), done.
From git://github.com/hanlab-SNU/pleio
   e065a06..14c3399  master     -> origin/master
Updating e065a06..14c3399
Fast-forward
 README.md       | 2 +-
 ldsc_preprocess | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

Tutorial

If you want to try a joint analysis of 18 characteristics of cardiovascular diseases using the PLEIO framework, please use the following link

Citation

If you use the software, please cite
Lee, C. H., Shi, H., Pasaniuc, B., Eskin, E., & Han, B. (2021). PLEIO: a method to map and interpret pleiotropic loci with GWAS summary statistics. The American Journal of Human Genetics, 108(1), 36–48.

Support

Issues with PLEIO? Email [email protected]

License

This project has no license currently.

Authors

Cue Hyunkyu Lee ( Seoul National University )