pygskit: A general-purpose Python package for the analysis of genetic data.

Overview

pygskit is a Python package designed for the analysis of genetic data using mostly Hail. This package is currently under development.

Key features

• Scalable join calling
• QC and filtering
• Computation of cohort-specific metrics (e.g., allele frequency)

Installing the Required Dependencies via Conda

git clone https://github.com/MedGenOL/pygskit
cd pygskit
conda env create -f environment.yml
conda activate pygskit
pip install . -r requirements.txt

Updating the package

cd pygskit
git pull origin main # update the source code from <main> branch
conda env update -f environment.yml # required only if the environment.yml file has been updated
conda activate pygskit
pip install . -r requirements.txt --upgrade

Maintainers

• Enrique Audain
• Rafiga Masmaliyeva