SAMtools MCP (Model Control Protocol)

A Model Control Protocol implementation for SAMtools, providing a standardized interface for working with SAM/BAM/CRAM files.

Features

View and convert SAM/BAM/CRAM files
Sort alignment files
Index BAM/CRAM files
Generate statistics
Merge multiple BAM files
Calculate read depth
Index FASTA files
And more...

Core Capabilities

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

Tools Overview

Tool	Description	Key Features
`view`	View and convert alignment files	- Format conversion (SAM/BAM/CRAM)- Region filtering- Flag-based filtering- Header manipulation
`sort`	Sort alignment files	- Coordinate-based sorting- Name-based sorting- Memory per thread control- Multi-threading support
`index`	Index BAM/CRAM files	- BAI index generation- CSI index support- CRAM index creation
`merge`	Merge multiple BAM/CRAM files	- Multi-file merging- Thread-enabled processing- Header reconciliation
`depth`	Calculate read depth	- Per-base depth calculation- Region-specific analysis- Multi-file support
`flagstat`	Generate alignment statistics	- Comprehensive flag statistics- Quality checks- Paired-end metrics
`idxstats`	BAM/CRAM index statistics	- Reference sequence stats- Mapped/unmapped counts- Length information
`faidx`	Index FASTA files	- FASTA indexing- Region extraction- Sequence retrieval

Installation

Using Docker (Recommended)

The easiest way to use SAMtools MCP is through Docker:

# Pull the Docker image
docker pull nadhir/samtools-mcp:latest

# Run the container
docker run -it --rm nadhir/samtools-mcp:latest

# To process BAM files, mount a volume:
docker run -it --rm -v /path/to/your/bam/files:/data nadhir/samtools-mcp:latest

Local Installation

Clone the repository:

git clone https://github.com/your-username/samtools_mcp.git
cd samtools_mcp

Install dependencies:

pip install uv
uv pip install -r requirements.txt

Configuration

MCP Server Configuration

To configure the MCP server to use the Docker image, add the following to your MCP configuration file:

{
  "servers": {
    "samtools": {
      "type": "docker",
      "image": "nadhir/samtools-mcp:latest",
      "volumes": [
        {
          "source": "/path/to/your/data",
          "target": "/data"
        }
      ]
    }
  }
}

Local MCP Configuration

To configure the MCP to run using uv, add the following to your ~/.cursor/mcp.json:

{
  "samtools_mcp": {
    "command": "uv",
    "args": ["run", "--with", "fastmcp", "fastmcp", "run", "/path/to/samtools_mcp.py"]
  }
}

Replace /path/to/samtools_mcp.py with the actual path to your samtools_mcp.py file.

Usage

Basic Commands

View BAM file:

from samtools_mcp import SamtoolsMCP

mcp = SamtoolsMCP()
result = mcp.view(input_file="/data/example.bam")

Sort BAM file:

result = mcp.sort(input_file="/data/example.bam", output_file="/data/sorted.bam")

Index BAM file:

result = mcp.index(input_file="/data/sorted.bam")

Advanced Usage

View specific region with flags:

result = mcp.view(
    input_file="/data/example.bam",
    region="chr1:1000-2000",
    flags_required="0x2",
    output_format="SAM"
)

Sort by read name:

result = mcp.sort(
    input_file="/data/example.bam",
    output_file="/data/namesorted.bam",
    sort_by_name=True
)

Calculate depth with multiple input files:

result = mcp.depth(
    input_files=["/data/sample1.bam", "/data/sample2.bam"],
    region="chr1:1-1000000"
)

Contributing

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

License

This project is licensed under the MIT License - see the LICENSE file for details.

This server cannot be installed

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security - not tested

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license - not tested

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quality - not tested