This repository contains the scripts to run the GoDMC pipeline which includes:
Please note the scripts in this repository are copyright of the Genetics of DNA Methylation Consortium and released with a GPL v3 license.
Genetics of DNA Methylation Consortium (GoDMC) is an international consortium of researchers interested in understanding the interplay between genetic and epigenetic variation. Our objective is to bring together researchers with matched genetic and DNA methylation data to consolidate resources and perform highly powered analyses to understand how both genetics and epigenetics influences health and disease. Outputs from the consortium will be made available to the research community.
To give you an idea of the kind of analyses we are interested please review our previous publication: https://pubmed.ncbi.nlm.nih.gov/34493871/.
If you are interested in joining or finding out more please contact either Josine Min (Josine.Min@bristol.ac.uk) or Eilis Hannon (E.J.Hannon@exeter.ac.uk)
Detailed instructions for running each stage of the pipeline can be found here. This includes details on how what software you need to have installed, and the required input data and their format.
Whilst we have done a lot of testing of these scripts across a range of different datasets, we do anticipate that there will be bugs and edge cases we are yet to detect. All communication regarding this pipeline is to occur through this GitHub repository. If you email any of the developers they will direct you back to this repository.
There are two ways to communicate with us.
Thank you for helping improve our project! Before you submit an issue, please take a moment to review these guidelines to ensure your issue is addressed effectively.
Search Existing Issues: Before submitting a new issue, please search the existing issues (including closed issues) to see if your problem has already been reported. This helps avoid duplicates and allows us to focus on a single thread of discussion for each issue.
Use Clear and Descriptive Titles: Provide a concise summary of the issue in the title. This helps others understand and search for similar issues.
Provide Detailed Information:
For Bugs: Specify which script you were running when the error occured, the expected result, and the actual result. Provide any relevant logs or screenshots.
For Documentation: Specify the page & section where the documentation was misleading or confusing.
The scripts in this repository were developed by the core GoDMC team and individuals who had approved external projects. A list can be found under the Acknowledgements section below. At present just this group are able to contribute to the pipeline - if you are interested in joining this group please contact either Josine Min (Josine.Min@bristol.ac.uk) or Eilis Hannon (E.J.Hannon@exeter.ac.uk).
The developer group of these scripts are listed in alphabetical order below:
Carlos Ruiz Arenas
Olalekan Awoniran
Eilis Hannon
Gibran Hemani
Josine Min
Maria Soler Artigas
Natalia Llonga
Olivia Castellini
Siyi Wang
Sonja Rajic
Thomas Jonkman
Xiaopu Zhang