Metadata-Version: 2.1
Name: varstrat
Version: 0.1.0
Summary: A tool to annotate VCF files using genome stratification files, targeting difficult regions.
Author: Thinh Quyen
Author-email: thinhquyen9461@gmail.com
Classifier: Programming Language :: Python :: 3
Classifier: License :: OSI Approved :: MIT License
Classifier: Operating System :: OS Independent
Requires-Python: >=3.9
Description-Content-Type: text/markdown
License-File: LICENSE

# VarStrat

A tool for annotating VCF files using genome stratification files, targeting difficult regions.

## Installation

Use the package manager [pip](https://pip.pypa.io/en/stable/) to install VarStrat.

```bash
pip install varstrat
```

## Usage
To use the tool from the command line:
```bash
varstrat input.vcf output.vcf data_source_dir
```


## Final Notes

1. **Make Sure the Script is Executable:**
   - Ensure `stratify.sh` is executable by running `chmod +x varstrat/stratify.sh`.
   - Also, make sure `stratify.py` is executable by running `chmod +x varstrat/stratify.py`.

2. **Verify the Help Option:**
   - Run your script with the `-h` or `--help` option to verify it displays the help message correctly:
     ```bash
     varstrat -h
     ```
