samtools_merge · Samtools MCP: Risk & Policy

WHAT IT DOES

What samtools_merge does on Samtools

AI agents use samtools_merge 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_merge needs a policy

This tool combines multiple input BAM/CRAM files into a single output file. This is a reversible write operation—the merged file can be recreated or deleted, and the original input files remain intact. It does not delete, destroy, or execute arbitrary code. While it modifies the filesystem by creating a new file, this is within the Write category.

From the tool's definition Tool name 'samtools_merge' and description 'Merge multiple sorted BAM/CRAM files' indicate creation of a new combined file from existing input files.

Attacks that exploit this kind of access

Recommended rule Ready

Verdict

samtools_merge Rate-limited

samtools_merge 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_merge": {
      "limits": [
        {
          "counter": "samtools_merge_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_merge

What does the samtools_merge tool do? +

Merge multiple sorted 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_merge? +

Register the Samtools MCP server in PolicyLayer and add a rule for samtools_merge: 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_merge? +

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

Can I rate-limit samtools_merge? +

Yes. Add a rate_limit block to the samtools_merge 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_merge completely? +

Set action: deny in the PolicyLayer policy for samtools_merge. 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_merge? +

samtools_merge 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.