SSF-morph

GWAS Summary Statistic Formatting and Validation Tool

Cannot run from file:// — This tool must be served from an HTTP server, not opened directly as a file. Run python -m http.server in this folder and open http://localhost:8000 instead.

Browser requirement: This tool requires a modern browser with WebAssembly support (Google Chrome, Microsoft Edge, Firefox, or Safari 15.4+).

File size limit: For best performance, please process files that are smaller than 2 GB here.

Format a GWAS summary statistics file

Step by step

Select your input file
Prepare the configuration file
Edit the configuration and test on the first 5 rows of your input
Apply the configuration to your whole file and download the formatted result

Validate a GWAS summary statistics file

Check against gwas-ssf schema

Select your input file
Validate your file and read the validation result

Select File

Configuration

Edit & Test

Apply

Step 1: Select the input file

Drop your input file below, or click to browse:

Drop file here or click to browse

Supports TSV, CSV, and other delimited formats (up to 2 GB)

Step 2: Prepare the configuration file

2.1 Specify the delimiter in the input file: If your file contains comment lines (for example, lines starting with #), please let us know which character is used to mark comments: (Leave empty if not applicable.)

2.2 Select the analysis software used to generate your data:

Step 3: Edit and test your configuration

Preview how the configuration reformats your data using the Test button, then adjust as needed.

Configuration:

Output file prefix

Field separator

Missing value text(blank = null)

Convert -log₁₀ p-value

Remove comments

Your output (first 5 rows):

Step 4: Apply configuration and download

Apply your configuration to the entire input file. The formatted output will be downloaded to your browser's default download folder.

Operation stopped. For large files, the offline CLI is much faster:
pip install gwas-sumstats-tools
gwas-ssf format -f <your-file> -c <config.json>
See formatting CLI docs

Validate your formatted file

Tip: For large files or repeated use, you can run the validator locally via the command-line tool. See how to install from PyPI.

5.1 Select the file to validate:

Drop file here or click to browse

5.2 Set validation thresholds (optional):
Minimum number of variants (rows): Allow zero p-values:

For GWAS Catalog submission, lower row numbers may be permissible in certain circumstances (please contact gwas-subs@ebi.ac.uk to request an eligibility review). For files containing zero p-values, analysis software type must be provided in the metadata template (see GWAS Catalog submission documentation for details).

5.3 Run validation:

First 1M rows — ~3 min

~5 min per 0.5 GB

or run locally via PyPI for faster results

Validation stopped. For large files, the offline CLI is much faster:
pip install gwas-sumstats-tools
gwas-ssf validate <your-file>
See validation CLI docs