AI agents call samtools_list_files to retrieve information from Samtools without modifying anything — typically the context-gathering step in research, monitoring, and reporting workflows, before the agent takes action elsewhere.
This tool retrieves and queries file information without side effects. It performs a passive listing operation, analogous to 'ls' or 'find', returning metadata about existing files. No data is created, modified, deleted, or executed, making it a Read category tool with low severity.
From the tool's definition Tool name 'samtools_list_files' and description 'List BAM/SAM/CRAM files in a directory' indicate directory enumeration and file discovery with no modification or execution.
Attacks that exploit this kind of access
List BAM/SAM/CRAM files in a directory. It is categorised as a Read tool in the Samtools MCP Server, which means it retrieves data without modifying state.
Register the Samtools MCP server in PolicyLayer and add a rule for samtools_list_files: 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.
samtools_list_files is a Read tool with low risk. Read-only tools are generally safe to allow by default.
Yes. Add a rate_limit block to the samtools_list_files 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.
Set action: deny in the PolicyLayer policy for samtools_list_files. 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.
samtools_list_files 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.
Every MCP server has a record like this.
Type a name, get the same breakdown: verified identity, auth posture, risk grade, capabilities, recommended policy.
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