# Samtools

> Use this tool when you need to interact with genomic data through SAM/BAM file operations, solving problems such as variant calling, read alignment, and genomic data analysis. It provides an interface for AI agents to input SAM/BAM files and output analyzed genomic data. This tool is ideal for use cases involving high-throughput sequencing data processing and analysis in bioinformatics and genomics research.

Canonical page: https://skillsregistry.net/skills/sirusb-samtools  
JSON: https://api.skillsregistry.net/v1/skills/sirusb-samtools

## Description

A Python implementation of the Model Context Protocol (MCP) for Samtools, allowing AI assistants to interact with genomic data through SAM/BAM file operations.

## Trust

- **Trust score (0–1):** 0.99
- **Verification tier:** verified
- **Last scanned:** 2026-09-19

## Facts

- **Version:** 1.0.0
- **Skill type:** atomic
- **Execution layer:** mcp-remote
- **Runtime environment:** api
- **Category:** file-system
- **Updated:** 2026-09-19

## Source

- **Source listing:** [PulseMCP](https://www.pulsemcp.com/servers/sirusb-samtools)
- **Repository:** <https://github.com/sirusb/samtools_mcp>

## Use it

Resolve this record through the SkillsRegistry MCP server (no auth, read-only):

```
claude mcp add --transport http --scope user skillsregistry https://api.skillsregistry.net/mcp
```

```json
{
  "jsonrpc": "2.0",
  "id": 1,
  "method": "tools/call",
  "params": {
    "name": "get_skill",
    "arguments": {
      "slug": "sirusb-samtools"
    }
  }
}
```

REST: `GET https://api.skillsregistry.net/v1/skills/sirusb-samtools` · pull for local use: `GET https://api.skillsregistry.net/v1/skills/sirusb-samtools/pull`

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SkillsRegistry indexes agent skills from public registries and GitHub. Skills we have analysed are scanned with Circle-IR and scored on six dimensions; each listing states its scan coverage. More: https://skillsregistry.net/llms.txt