samtools_index · Samtools MCP: Risk & Policy

WHAT IT DOES

What samtools_index does on Samtools

AI agents use samtools_index to create or update resources in Samtools — usually the action step of a workflow, after the agent has gathered context. Every call changes real data in your Samtools environment.

WHY IT NEEDS A POLICY

Why samtools_index needs a policy

This tool creates an index file (.bai/.csi/.crai) alongside an existing SAM/BAM/CRAM file. It creates new files (index files) without modifying the original data file, making it a Write operation. The blast radius is low since it only adds index files and does not alter the original genomic data.

From the tool's definition Index SAM/BAM/CRAM files

Attacks that exploit this kind of access

Recommended rule Ready

Verdict

samtools_index Rate-limited

samtools_index stays usable, but capped — an agent stuck in a loop can't make hundreds of changes a minute. Everything else on the server is denied unless you say otherwise.

View as policy code

policy.json

{
  "version": "1",
  "default": "deny",
  "tools": {
    "samtools_index": {
      "limits": [
        {
          "counter": "samtools_index_rate",
          "window": "minute",
          "max": 30,
          "scope": "grant"
        }
      ]
    }
  }
}

LIMIT THIS TOOL →

Instant setup, no code required.

PolicyLayer is an MCP gateway: every tool call is checked against your rule before it reaches Samtools, so you can run agents against it safely.

FAQ

Questions about samtools_index

What does the samtools_index tool do? +

Index SAM/BAM/CRAM files. It is categorised as a Write tool in the Samtools MCP Server, which means it can create or modify data. Consider rate limits to prevent runaway writes.

How do I enforce a policy on samtools_index? +

Register the Samtools MCP server in PolicyLayer and add a rule for samtools_index: allow, deny, rate-limit, or require approval. Point your MCP client at the PolicyLayer proxy URL and the rule is enforced on every call, before it reaches Samtools. Nothing to install.

What risk level is samtools_index? +

samtools_index is a Write tool with medium risk. Write tools should be rate-limited to prevent accidental bulk modifications.

Can I rate-limit samtools_index? +

Yes. Add a rate_limit block to the samtools_index rule in your PolicyLayer policy. For example, setting max: 10 and window: 60 limits the tool to 10 calls per minute. Rate limits are tracked per agent session and reset automatically.

How do I block samtools_index completely? +

Set action: deny in the PolicyLayer policy for samtools_index. The AI agent will receive a policy violation error and cannot call the tool. You can also include a reason field to explain why the tool is blocked.

What MCP server provides samtools_index? +

samtools_index is provided by the Samtools MCP server (sirusb/samtools_mcp). PolicyLayer sits as a proxy in front of this server to enforce policies before tool calls reach the server.