// SCAN REPORT

Samtools

9 tools. 4 can modify or destroy data without limits.

4 write tools that can modify data. Rate limits recommended.

Last updated: 5 Jul 2026

4 can modify or destroy data

5 read-only

9 tools total

Community server · catalogue entry verified 05/07/2026

How to control Samtools ↓

TOOL MAP

What Samtools exposes to your agents

Read (5) Write / Execute (4) Destructive / Financial (0)

Running more than one server? Check your whole stack →

MOST DANGEROUS TOOLS

High Risk

The most dangerous Samtools tools

Execute · High samtools_view samtools view is a well-known bioinformatics command that can both read/filter SAM/BAM/CRAM files and write converted output files. Write · Medium samtools_merge This tool combines multiple input BAM/CRAM files into a single output file. Write · Medium samtools_faidx This tool has dual functionality: (1) indexing FASTA files, which writes a new .fai index file to disk (a Write operation), and (2) extracting/reading sequences from an already-indexed FASTA (a Read operation). Write · Low samtools_index This tool creates an index file (.bai/.csi/.crai) alongside an existing SAM/BAM/CRAM file.

4 of Samtools's 9 tools can modify, destroy, or commit something on every call — and an agent calls them with no built-in limits.

POLICY

How to control Samtools

PolicyLayer is an MCP gateway — it sits between your AI agents and Samtools, and nothing reaches the server without passing your rules. These are the rules we recommend:

Rate limit write operations

{
  "samtools_faidx": {
    "limits": [
      {
        "counter": "samtools_faidx_per_hour",
        "window": "hour",
        "max": 30,
        "scope": "grant"
      }
    ]
  }
}

Prevents bulk unintended modifications from agents caught in loops.

Cap read operations

{
  "samtools_depth": {
    "limits": [
      {
        "counter": "samtools_depth_per_minute",
        "window": "minute",
        "max": 60,
        "scope": "grant"
      }
    ]
  }
}

Controls API costs and prevents retry loops from exhausting upstream rate limits.

Create a free account and register Samtools — nothing to install.
Add these rules — paste them, or build them visually. Tune the limits to your setup.
Point your MCP client (Claude, Cursor, anything) at your gateway URL.

ENFORCE POLICY ON SAMTOOLS →

Instant setup, no code required.

FULL CATALOGUE

All 9 Samtools tools

EXECUTE 1 tools

Execute samtools_view samtools_view

WRITE 3 tools

Write samtools_faidx Index FASTA files or extract sequences from indexed FASTA. Write samtools_index Index SAM/BAM/CRAM files. Write samtools_merge Merge multiple sorted BAM/CRAM files.

READ 5 tools

Read samtools_depth samtools_depth Read samtools_flagstat Generate statistics on a BAM/CRAM file. Read samtools_idxstats Generate statistics from a BAM/CRAM index. Read samtools_list_files List BAM/SAM/CRAM files in a directory. Read samtools_sort samtools_sort

FAQ

Questions about Samtools

How do I prevent bulk modifications through Samtools? +

The Samtools server has 3 write tools including samtools_faidx, samtools_index, samtools_merge. Set a rate limit in your policy -- for example, 10 calls per hour prevents an agent from making more than 10 modifications per hour. PolicyLayer enforces this at the gateway, before calls reach Samtools.

How many tools does the Samtools MCP server expose? +

9 tools across 2 categories: Read, Write. 5 are read-only. 4 can modify, create, or delete data.

How do I enforce a policy on Samtools? +

Register the Samtools MCP server in PolicyLayer, apply the suggested rules above (adjust the limits to your use case), and point your AI client at the PolicyLayer proxy URL instead of the server directly. Your agents keep the same tools; PolicyLayer evaluates every call against policy before it executes. Nothing to install, live in minutes.

Enforce policy on every Samtools tool call.

Deterministic rules across all 9 Samtools tools. Per-identity grants. Full audit log. Live in minutes. Nothing to install.

ENFORCE POLICY ON SAMTOOLS →

Instant setup, no code required.

9 Samtools tools catalogued and risk-classified — across an index of 43,000+ MCP servers.