Samtools

🚀 SAMtools MCP (Model Control Protocol)

A standardized interface implementation for SAMtools to handle SAM/BAM/CRAM files.

✨ Features

• View and convert SAM/BAM/CRAM files
• Sort alignment files
• Index BAM/CRAM files
• Generate statistical information
• Merge multiple BAM files
• Calculate read depth
• Index FASTA files
• And many more features...

Core Capabilities

• File Format Support: Handle SAM (text), BAM (binary), and CRAM (compressed) alignment files.
• Format Conversion: Seamlessly convert between SAM, BAM, and CRAM formats.
• Region-Specific Analysis: Extract and analyze specific genomic regions.
• Flag Filtering: Filter based on SAM flags.
• Performance Optimization: Multi-threaded operations for sorting and merging.
• Statistical Analysis: Generate comprehensive alignment statistics.

Tool Overview

📦 Installation

Install with Docker

# Download and run the SAMtools image
docker pull samtools/gatk4:latest
docker run -it samtools/gatk4:latest

Local Installation

1. Visit the SAMtools download page.
2. Select the appropriate version for your system and compile and install it.

Configuration

Docker Configuration

{
    "version": "0.1",
    "services": {
        "samtools": {
            "image": "samtools/gatk4:latest",
            "container_name": "samtools-service",
            "restart": "always"
        }
    }
}

Local Configuration (Example)

# Configure environment variables
export PATH=/path/to/samtools:$PATH

# Create a configuration file
touch ~/.config/samtools/config.json

💻 Usage Examples

Basic Usage

# View alignment files
samtools view -h input.bam | less

# Sort alignment files
samtools sort input.bam output.sorted

# Index sorted files
samtools index output.sorted.bam

Advanced Usage

# Merge multiple BAM files
samtools merge -f output.bam sample1.bam sample2.bam

# Calculate read depth for a specific region
samtools depth -r chr1:1-1000000 merged.bam > depth.txt

🤝 Contribution Guidelines

Contributions are welcome! Please feel free to submit a Pull Request.

📄 License

This project is licensed under the MIT License. Please refer to the LICENSE file for detailed information.