GWAS SumStats Tools

GWAS SumStats Tools is a versatile toolkit created to simplify the processing, validation, and formatting of GWAS summary statistics files intended for submission to the GWAS Catalog. This toolkit provides a variety of features designed for efficiency and ease of use.

Features

Reading: Preview a GWAS summary statistics data file, extract headers, metadata, or specific field-value pairs from the metadata.
Formatting: Convert tabular summary statistics files to GWAS Catalog standard format (gwas-ssf), with options for splitting fields, renaming fields, reordering, converting -log (P-value) to normal P-values, handling missing values efficiently and removing comments.
Metadata Generation: Automatically generate metadata for a data file from a submission form or create metadata from the GWAS Catalog (for internal use).
Validation: Validate the integrity of a summary statistic file using a dynamically generated schema.

Quick Start

User-friendly Interface: SSF-morph

If you prefer a user-friendly interface for formatting or validating your data, you can use our online tool. This interface allows you to quickly format or validate individual files with a size limit of 2 GB, all without the need for command-line usage. Simply click SSF-morph to access the tool and upload your data directly from your local computer.

For instructions on how to use the SSF-morph, please visit our UI Guide Page.

Tip

Please note that this interface works with a single file only and has a file size limitation of 2GB .

Command Line Interface

However, if you require full access to all functions, or if you need to process larger files or multiple files simultaneously, we recommend using the command-line interface. Please follow the instructions provided here to install and use the command-line tools.

Local Installation with pip

Installation requirements: Python version 3.9 to 3.11.

$ pip3 install gwas-sumstats-tools
$ gwas-ssf --help