A categorical variation call to action

Note: This repository is under active development.

This repository contains code for analyses pertaining to A Categorical Variant Call to Action. Here, we intend to provide a broad background of the presence of categorical variants within genomic knowledge bases.

Supporting analyses include:

• Variant types in CIViC
• Multiple expressions per Allele ID in ClinVar
• Counts of NTRK fusions curated by COSMIC
• FDA oncology approvals being indicated for categories of genomic variants

Installation

Download

This repository can be downloaded through GitHub by either using the website or terminal. To download on the website, navigate to the top of this page, click the green Clone or download button, and select Download ZIP to download this repository in a compressed format. To install using GitHub on terminal, type:

git clone ga4gh/2025-catvar-call-to-action
cd 2025-catvar-call-to-action

Python dependencies

This repository uses Python 3.12. We recommend using a virtual environment and running Python with conda-forge.

Run the following from this repository's directory to create a virtual environment and install dependencies with Anaconda or Miniconda:

conda create -y -n 2025-catvar-call-to-action python=3.12 -c conda-forge
conda activate 2025-catvar-call-to-action
pip install -r requirements.txt

Or, if using base Python:

virtualenv venv
source activate venv/bin/activate
pip install -r requirements.txt

To make the virtual environment available to jupyter notebooks, execute the following code while the virtual environment is activated:

pip install jupyter
ipython kernel install --user --name=2025-catvar-call-to-action