GWASpy

Genome-wide association studies pypeline (GWASpy): A Python package for performing GWAS QC, PCA, haplotype phasing, and genotype imputation.

Installation

GWASpy is available through PyPI. To install, run the command:

pip3 install gwaspy

For usage, please visit GWASpy

GWASpy is generously distributed under the MIT License

Name	Name	Last commit message	Last commit date
Latest commit z-koenig updated argparse ref path in pca.py Mar 25, 2025 506c572 · Mar 25, 2025 History 445 Commits
.github/workflows	.github/workflows	python-version 3.9 was throwing ModuleNotFoundError for numpy	Jan 27, 2025
docs	docs	update docs to include GLIMPSE Hail Batch example	Feb 5, 2025
gwaspy	gwaspy	updated argparse ref path in pca.py	Mar 25, 2025
nf	nf	minor updates	Jan 30, 2025
.DS_Store	.DS_Store	updated ref path in pca.py	Mar 25, 2025
.gitattributes	.gitattributes	uploaded 1KG PCA test dataset	Apr 28, 2021
.readthedocs.yml	.readthedocs.yml	declare python requirements required to build the docs	Jan 31, 2025
Dockerfile	Dockerfile	install makeScaffold for building haplotype scaffolds for phasing	Jun 10, 2022
LICENSE	LICENSE	Create LICENSE	Jan 27, 2022
README.md	README.md	minor install updates	May 16, 2022
TODO.md	TODO.md	use GWASpy as the name	May 26, 2021
env-setup.sh	env-setup.sh	we no longer need to install git lfs during build as GWASpy has no data	Dec 13, 2021
requirements.txt	requirements.txt	revert back to explicit packages in install_requires	Jan 27, 2025
setup.py	setup.py	add moduel for checking and fixing possible allele flips	Jan 31, 2025
split_maps.sh	split_maps.sh	script for splitting map files by CHROM when building Docker image	Aug 4, 2021