BAMCP

RTrentJones/BAMCP

★ 0 stars Python AI/LLM Updated 2d ago

An MCP server for viewing and interacting with genomic data for BAM and eventually CRAM files using MCP apps.

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Quick Install

Copy the config for your editor. Some servers may need additional setup — check the README.

Add to claude_desktop_config.json:

{
  "mcpServers": {
    "bamcp": {
      "command": "uvx",
      "args": [
        "bamcp"
      ]
    }
  }
}

Or install with pip: pip install bamcp

README Excerpt

**Interactive BAM/CRAM variant visualization for AI assistants via the Model Context Protocol** BAMCP brings IGV-style alignment visualization directly into your AI conversations. Browse BAM/CRAM files, inspect variant evidence, and navigate genomic regions—all through natural language interaction with Claude or other MCP-enabled assistants.

Tools (20)

BAMCP_AUTH_ENABLEDBAMCP_DEFAULT_WINDOWBAMCP_HOSTBAMCP_ISSUER_URLBAMCP_MAX_READSBAMCP_MIN_DEPTHBAMCP_MIN_MAPQBAMCP_MIN_VAFBAMCP_PORTBAMCP_REFERENCEBAMCP_REQUIRED_SCOPESBAMCP_RESOURCE_SERVER_URLBAMCP_TOKEN_EXPIRYBAMCP_TRANSPORTcleanup_cachefile_pathget_coverageget_region_summaryget_variant_curation_summaryget_variants

BAMCP

Quick Install

README Excerpt

Tools (20)

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