https://github.com/kris96tian/vcf-snp-analysis-app
Web application for analyzing VCF (Variant Call Format) files containing genetic variants such as SNPs (Single Nucleotide Polymorphisms).
https://github.com/kris96tian/vcf-snp-analysis-app
plotly snps vcf-files
Last synced: 4 months ago
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Web application for analyzing VCF (Variant Call Format) files containing genetic variants such as SNPs (Single Nucleotide Polymorphisms).
- Host: GitHub
- URL: https://github.com/kris96tian/vcf-snp-analysis-app
- Owner: kris96tian
- Created: 2025-02-26T17:15:30.000Z (8 months ago)
- Default Branch: main
- Last Pushed: 2025-02-27T19:36:17.000Z (8 months ago)
- Last Synced: 2025-05-05T07:52:06.342Z (6 months ago)
- Topics: plotly, snps, vcf-files
- Language: Python
- Homepage: https://vcfanalysis.pythonanywhere.com/
- Size: 24.4 KB
- Stars: 0
- Watchers: 1
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
Awesome Lists containing this project
README
# VCF/SNP Analyzer App
Link to the Web-App: https://vcfanalysis.pythonanywhere.com/
A Flask web application for analyzing VCF (Variant Call Format) files containing genetic variants such as SNPs (Single Nucleotide Polymorphisms).
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## Features
- Upload and validate VCF files (supports .vcf, .vcf.gz, and .bcf formats)
- Automatic fixing of common VCF format issues
- Comprehensive variant analysis including:
- Variant type distribution
- Chromosome distribution
- Quality score distribution
- Transition/Transversion ratio
- Population genetics metrics
- Interactive visualizations using Plotly
- Asynchronous processing of large files with job status tracking
## Installation
### Prerequisites
- Python 3.8+
- pip
### Setup
1. Clone this repository:
```bash
git clone https://github.com/yourusername/snp-analyzer-app.git
cd snp-analyzer-app
```
2. Create and activate a virtual environment:
```bash
python -m venv venv
source venv/bin/activate # On Windows: venv\Scripts\activate
```
3. Install dependencies:
```bash
pip install -r requirements.txt
```
## Usage
1. Start the application:
```bash
python app.py
```
2. Open your web browser and navigate to `http://127.0.0.1:5000/`
3. Upload a VCF file:
- Click on "Choose File" and select a VCF file
- Click "Analyze File" to process the file and view results
- Alternatively, click "Validate Only" to check if the file is valid without running analysis
4. View analysis results:
- Chromosome distribution visualization
- Quality score distribution
- Variant type statistics
- Ts/Tv ratio and other metrics
## Technical Details
- **Backend**: Flask (Python)
- **Data Processing**: cyvcf2, numpy
- **Frontend**: HTML, JavaScript, Tailwind CSS
- **Visualization**: Plotly
- **File Management**: Only temporary files used during processing (no persistent storage)
## Development
To contribute to this project:
1. Fork the repository
2. Create a feature branch: `git checkout -b feature-name`
3. Commit your changes: `git commit -am 'Add some feature'`
4. Push to the branch: `git push origin feature-name`
5. Submit a pull request