🧬 Variant Analysis Pipeline

This repository presents a mock variant analysis pipeline simulating key steps of DNA sequencing data analysis using Python. It integrates four main components:

1. Quality Control – Simulated FastQC
2. Alignment – Simulated BWA output
3. Variant Calling – Mocked GATK variant calling
4. Variant Annotation – Mock VEP annotations

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📌 Key Features

• ✅ Single Python script to simulate the full workflow
• 📁 Pre-loaded input files (sample FASTQ and reference genome)
• 🧪 Simulated output files mimicking real tools like FastQC, BWA, GATK, and VEP
• 🧰 No external dependencies (easy to run, no installations needed)
• 📦 Clean project structure ready for GitHub portfolio
• 👩‍💻 Beginner-friendly and useful for learning how pipelines work

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▶️ How to Run

git clone https://github.com/yourusername/variant-analysis-pipeline.git
cd variant-analysis-pipeline
pip install -r requirements.txt
python variant_pipeline.py

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📁 Output Files

All results are saved in the output/ folder:

• fastqc_report.html: Simulated QC report
• aligned.bam: Fake alignment output
• variants.vcf: Simulated variant calls
• annotated.txt: Fake annotated variant list

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📂 Project Structure

variant-analysis-pipeline/
├── data/               # Input files
├── output/             # Results from each step
├── variant_pipeline.py # Main script
└── README.md

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💡 Disclaimer

This is a mock implementation designed for portfolio/demo purposes. Tools like FastQC, BWA, GATK, and VEP are referenced but not actually used.

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👩‍💻 Author

Dhanyashri A/P Guruparan