GWASStudio: A Tool for Genomic Data Management

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Overview

GWASStudio is a powerful CLI tool designed for efficient storage, retrieval, and querying of genomic summary statistics. It offers a high-performance infrastructure for handling and analyzing large-scale GWAS and QTL datasets, enabling seamless cross-dataset exploration.

Please see the documentation at https://ht-diva.github.io/gwasstudio/

Core Purpose

GWASStudio provides a unified interface across the CDH infrastructure, handling the ingestion, storage, querying and export of genomic data using high-performance technologies.

Key Functionalities

GWASStudio consists of several key functionalities:

1. Data Ingestion

Data Ingestion: Imports summary statistics data and its metadata associated.
Support for Multiple Storage Options: Works with both local filesystems and cloud storage (S3).

2. Data Querying

Flexible Search: Enables searching metadata using template files.

3. Data Export

Selective Export: Extracts subsets of data and its metadata associated based on genomic regions, SNPs, or the entire set of data.

Technical Architecture

GWASStudio leverages several advanced technologies:

TileDB Embedded: A high-performance array storage engine that enables efficient storage and retrieval of genomic data.
MongoDB: A flexible, scalable NoSQL database used for storing and querying metadata associated with genomic datasets.
Dask: Provides distributed computing capabilities for processing large datasets.
Python Ecosystem: Built on Python with libraries like Click/Cloup for CLI interfaces, Pandas for data manipulation, and various genomics-specific tools.

Installation

For detailed installation instructions, please refer to the documentation at https://ht-diva.github.io/gwasstudio/

Usage

For detailed instructions on how to use this tool, please refer to the documentation and check the cli_test scripts for a practical guide by examples.

Citation

Example files are derived from:

The variant call format provides efficient and robust storage of GWAS summary statistics. Matthew Lyon, Shea J Andrews, Ben Elsworth, Tom R Gaunt, Gibran Hemani, Edoardo Marcora. bioRxiv 2020.05.29.115824; doi: https://doi.org/10.1101/2020.05.29.115824

Metadata

Release files for gwasstudio 3.3.0

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Source distribution (sdist)

Source distribution for gwasstudio 3.3.0
File	Size	Uploaded
gwasstudio-3.3.0.tar.gz	62.1 kB	Sep 11, 2026	Details

Built distribution (wheel)

Table of built distributions (wheels) for gwasstudio 3.3.0
File	Interpreter	ABI	Platform	Reset
gwasstudio-3.3.0-py3-none-any.whl 77.1 kB Sep 11, 2026	Python 3	none	any	Details

Total release size: 139.2 kB

Release files / gwasstudio-3.3.0.tar.gz

Download URL	gwasstudio-3.3.0.tar.gz
Size	62.1 kB
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SHA-256 checksum How to use checksums	`e53b5f336d1826573800d9d836facca0b2c2c1502ce2085a4a074cced3d1505e`
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Uploaded via	`twine/7.0.0 CPython/3.13.14`

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Publishing platform: GitHub Actions
Publishing repository: github.com/ht-diva/gwasstudio
Publishing commit: github.com/ht-diva/gwasstudio/tree/b6e7a0044ee0642b7958eac6d05c7448c2ca194d

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Publishing configuration: github.com/ht-diva/gwasstudio/blob/b6e7a0044ee0642b7958eac6d05c7448c2ca194d/.github/workflows/release.yml
Publishing logs: github.com/ht-diva/gwasstudio/actions/runs/34597460147/attempts/1

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Subject: gwasstudio-3.3.0.tar.gz
SHA-256 checksum: e53b5f336d1826573800d9d836facca0b2c2c1502ce2085a4a074cced3d1505e Verifying attestations

Release files / gwasstudio-3.3.0-py3-none-any.whl

Download URL	gwasstudio-3.3.0-py3-none-any.whl
Size	77.1 kB
Tags	Python 3
SHA-256 checksum How to use checksums	`400a001aad52959d9cc0dbe5b95e30d28f82b3791f86782fe5b7f33d246638d0`
BLAKE2b-256 checksum How to use checksums	`7a33fb5599304d6071ef46c2bcb122a019f5c0898f42ea0e3693a943638003e9`
Upload date	Sep 11, 2026
Uploaded using Trusted Publishing? What is trusted publishing?	Yes
Uploaded via	`twine/7.0.0 CPython/3.13.14`

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Identity

Publishing platform: GitHub Actions
Publishing repository: github.com/ht-diva/gwasstudio
Publishing commit: github.com/ht-diva/gwasstudio/tree/b6e7a0044ee0642b7958eac6d05c7448c2ca194d

Workflow

Publishing configuration: github.com/ht-diva/gwasstudio/blob/b6e7a0044ee0642b7958eac6d05c7448c2ca194d/.github/workflows/release.yml
Publishing logs: github.com/ht-diva/gwasstudio/actions/runs/34597460147/attempts/1

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Subject: gwasstudio-3.3.0-py3-none-any.whl
SHA-256 checksum: 400a001aad52959d9cc0dbe5b95e30d28f82b3791f86782fe5b7f33d246638d0 Verifying attestations