samtools_view · Samtools MCP: Risk & Policy

WHAT IT DOES

What samtools_view does on Samtools

AI agents invoke samtools_view to trigger actions in Samtools. What it does depends on the arguments the agent supplies, and its effects often reach beyond the immediate call — builds kicked off, notifications sent, workflows started.

WHY IT NEEDS A POLICY

Why samtools_view needs a policy

samtools view is a well-known bioinformatics command that can both read/filter SAM/BAM/CRAM files and write converted output files. Since the description is empty, the exact behavior is uncertain, but the canonical samtools view can execute file conversions and filtering operations with significant data transformation side effects.

From the tool's definition Tool name 'samtools_view' and server context of SAMtools MCP implementation for SAM/BAM/CRAM files. Description is empty.

Attacks that exploit this kind of access

Recommended rule Ready

Verdict

samtools_view Rate-limited

samtools_view stays usable, but rate-capped — a runaway agent can't fire it dozens of times 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_view": {
      "limits": [
        {
          "counter": "samtools_view_rate",
          "window": "minute",
          "max": 10,
          "scope": "grant"
        }
      ]
    }
  }
}

RATE-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_view

What does the samtools_view tool do? +

samtools_view. It is categorised as a Execute tool in the Samtools MCP Server, which means it can trigger actions or run processes. Use rate limits and argument validation.

How do I enforce a policy on samtools_view? +

Register the Samtools MCP server in PolicyLayer and add a rule for samtools_view: 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_view? +

samtools_view is a Execute tool with high risk. Execute tools should be rate-limited and have argument validation enabled.

Can I rate-limit samtools_view? +

Yes. Add a rate_limit block to the samtools_view 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_view completely? +

Set action: deny in the PolicyLayer policy for samtools_view. 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_view? +

samtools_view 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.