COSGAP: COntainerized Statistical Genetics Analysis Pipelines

Documentation

The main documentation for COSGAP is hosted at cosgap.rtfd.io

Project status

Information

The goal of this GitHub repository (https://github.com/comorment/containers) is to distribute software tools for statistical genetics analysis, alongside their respective reference data and scripts ("analysis pipelines") to facilitate the application of these tools. The scope of this project is currently limited to genome-wide association studies (GWAS) and post-GWAS statistical-genetics analyses, including polygenic scoring (PGS). This project builds on earlier work by Tryggve consortium, with the most recent major development done as part of the CoMorMent EU H2020 project (comorment.eu). For more information see our preprint manuscript, this presentation on PGC WWL meeting (Feb 9, 2024), or our online documentation here.

For an overview of available software, see here.

Most of these tools are packaged into singularity containers (https://sylabs.io/singularity/) and shared in the singularity folder of this repository. You can download individual containers using GitHub's Download button, or clone the entire repository from the command line as described in the INSTALL.md file.

Many of the tools require additional reference data provided in the reference folder of this repository. Certain reference data can not be made publicly available, in which case we provide access instructions in a separate GitHub repository: https://github.com/comorment/reference. This repository is private - please approach your contact within the CoMorMent project to enable your access.

Description of containers and usage instructions are provided in the docs folder.

More extensive use cases of containers, focusing on real data analysis, are provided in the usecases folder.

The history of changes is available in the CHANGELOG.md file.

If you would like to contribute to developing these containers, please see the CONTRIBUTING file.

Additional tools are available in separate repositories:

https://github.com/comorment/ldsc - LD score regression
https://github.com/comorment/mixer - cross-trait MiXeR analysis
https://github.com/comorment/popcorn - cross-ancestry genetic correlations
https://github.com/comorment/magma - MAGMA, LAVA, lava-partitioning tools
https://github.com/comorment/HDL - High-Definition Likelihood
https://github.com/comorment/ldpred2_ref - reference files for LDpred2. The tool itself is included in r.sif (more info).

Cite

If you use the software provided here, please cite our Zenodo.org code deposit (change version accordingly):

Oleksandr Frei, Andreas Jangmo, Espen Hagen, bayramakdeniz, ttfiliz, Richard Zetterberg, & John Shorter. (2024). comorment/containers: Comorment-Containers-v1.8.1 (v1.8.1). Zenodo. https://doi.org/10.5281/zenodo.10782180

Bibtex format:

@software{oleksandr_frei_2024_10782180,
  author       = {Oleksandr Frei and
                  Andreas Jangmo and
                  Espen Hagen and
                  bayramakdeniz and
                  ttfiliz and
                  Richard Zetterberg and
                  John Shorter},
  title        = {comorment/containers: Comorment-Containers-v1.8.1},
  month        = mar,
  year         = 2024,
  publisher    = {Zenodo},
  version      = {v1.8.1},
  doi          = {10.5281/zenodo.10782180},
  url          = {https://doi.org/10.5281/zenodo.10782180}
}

Please also cite our preprint:

Akdeniz, B.C., Frei, O., Hagen, E., Filiz, T.T., Karthikeyan, S., Pasman, J.A., Jangmo, A., Bergsted, J., Shorter, J.R., Zetterberg, R., Meijsen, J.J., Sønderby, I.E., Buil, A., Tesli, M., Lu, Y., Sullivan, P., Andreassen, O.A., & Hovig, E. (2022). COGEDAP: A COmprehensive GEnomic Data Analysis Platform. arXiv:2212.14103 [q-bio.GN]. DOI: [10.48550/arXiv.2212.14103](https://doi.org/)

Bibtex format:

@misc{akdeniz2022cogedap,
      title={COGEDAP: A COmprehensive GEnomic Data Analysis Platform}, 
      author={Bayram Cevdet Akdeniz and Oleksandr Frei and Espen Hagen and Tahir Tekin Filiz and Sandeep Karthikeyan and Joelle Pasman and Andreas Jangmo and Jacob Bergsted and John R. Shorter and Richard Zetterberg and Joeri Meijsen and Ida Elken Sonderby and Alfonso Buil and Martin Tesli and Yi Lu and Patrick Sullivan and Ole Andreassen and Eivind Hovig},
      year={2022},
      eprint={2212.14103},
      archivePrefix={arXiv},
      primaryClass={q-bio.GN}
}

Note that this project will soon be renamed "COSGAP", and that the citation info will be updated accordingly.

Installation

Please confer the INSTALL.md file for installation instructions.

Legacy

Earlier versions (prior to April 2021) of all containers and reference data were distributed via Google Drive. This is no longer the case, the folder on Google Drive is no longer maintained. All containers and reference data are released through this repository.

Source files

The source files for configuring and building the container files provided here are found in the docker directory. See the corresponding README file therein for details.

Documentation build instructions

The online documentation hosted at cosgap.rtfd.io can be built locally using Sphinx in a conda environment as

cd sphinx-docs/source  # documentation source/config directory
conda env create -f environment.yml  # creates environment "sphinx"
conda activate sphinx
make html  # make html-documentation in $PWD/_build/html/

The resulting file(s) $PWD/_build/html/index.html can be viewed in any web browser. In order to make a pdf with the documentation, issue

make pdflatex

and open $PWD/_build/latex/cosgap.pdf in a pdf viewer.

comorment / containers

readme