ld_pruning · Gwas MCP: Risk & Policy

WHAT IT DOES

What ld_pruning does on Gwas

AI agents invoke ld_pruning to trigger actions in Gwas. 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 ld_pruning needs a policy

The tool performs a computational operation (LD pruning) that filters/removes variants from a dataset to produce a reduced independent set. While 'removes' suggests data modification, this is a standard bioinformatics processing step that typically writes a new filtered output rather than irreversibly deleting source data.

From the tool's definition 'Prune SNPs based on linkage disequilibrium (LD). Removes variants in high LD to create an independent set.'

Attacks that exploit this kind of access

Recommended rule Ready

Verdict

ld_pruning Rate-limited

ld_pruning 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": {
    "ld_pruning": {
      "limits": [
        {
          "counter": "ld_pruning_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 Gwas, so you can run agents against it safely.

FAQ

Questions about ld_pruning

What does the ld_pruning tool do? +

Prune SNPs based on linkage disequilibrium (LD). Removes variants in high LD to create an independent set. It is categorised as a Execute tool in the Gwas MCP Server, which means it can trigger actions or run processes. Use rate limits and argument validation.

How do I enforce a policy on ld_pruning? +

Register the Gwas MCP server in PolicyLayer and add a rule for ld_pruning: 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 Gwas. Nothing to install.

What risk level is ld_pruning? +

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

Can I rate-limit ld_pruning? +

Yes. Add a rate_limit block to the ld_pruning 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 ld_pruning completely? +

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

ld_pruning is provided by the Gwas MCP server (muslus/gwas-mcp). PolicyLayer sits as a proxy in front of this server to enforce policies before tool calls reach the server.