Genomics MCP

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normalize_variant

Read-only

Resolves VCF, HGVS, or rsID input to canonical variants on an explicit genome assembly and records each step for traceable reproducibility.

Instructions

Normalize a variant (VCF-style, HGVS or rsID) on an explicit assembly with a trace. Available for: default.

Input Schema

TableJSON Schema

Name	Required	Description
`hgvs`	No
`rsid`	No
`sources`	No	Source names; default all available.
`variant`	No
`assembly`	No
`reference`	No

Output Schema

TableJSON Schema

Name	Required	Description	Default
`data`	No
`error`	No	Set when status is error.
`errors`	No	Per-source failures in partial results.
`limits`	No
`status`	Yes
`warnings`	No
`operation`	Yes
`provenance`	No
`truncation`	No
`source_status`	No
`schema_version`	No		1
`metadata_omitted`	No	Entries dropped from provenance/source_status/errors/warnings (or text shortened) to fit max_response_bytes. Absent when metadata is complete.

Schema Changelog

Changes observed during successful MCP inspections.

Changed1 schema field changedv0.1.1Sep 28, 2026

addedOutput schema / properties / metadata_omitted

Added value: +{
+  "anyOf": [
+    {
+      "additionalProperties": {
+        "type": "integer"
+      },
+      "type": "object"
+    },
+    {
+      "type": "null"
+    }
+  ],
+  "default": null,
+  "description": "Entries dropped from provenance/source_status/errors/warnings (or text shortened) to fit max_response_bytes. Absent when metadata is complete.",
+  "title": "Metadata Omitted"
+}

First observedv0.1.0Sep 24, 2026

TDQS

C2.8/5.0

Behavior2/5

Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?

Annotations already declare readOnlyHint and openWorldHint, and the description adds only the vague phrase 'with a trace' plus 'on an explicit assembly'. It never says what the trace contains, whether remote source lookups occur, or what a failed normalization looks like — gaps that matter for an open-world, multi-source resolver.

Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.

Conciseness3/5

Is the description appropriately sized, front-loaded, and free of redundancy?

The core sentence is tight and front-loaded with the action, which is good. The appended 'Available for: default' clause is unexplained boilerplate that adds noise without information.

Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.

Completeness2/5

Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?

With six optional parameters and three apparently alternative input forms, the description never states that you supply exactly one of variant/hgvs/rsid, nor how assembly applies to each. An output schema exists so return values need not be described, but the invocation contract is left ambiguous.

Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.

Parameters3/5

Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?

Schema description coverage is only 17%, so the burden largely falls on the description. It helpfully maps the recognized input forms (VCF-style/HGVS/rsID) onto variant/hgvs/rsid and flags the assembly requirement, but says nothing about whether inputs are mutually exclusive, how rsid is resolved, or what the reference FileRef is for.

Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.

Purpose4/5

Does the description clearly state what the tool does and how it differs from similar tools?

States a clear verb+resource ('Normalize a variant') and enumerates the accepted input forms (VCF-style, HGVS, rsID), which is genuinely informative. It does not differentiate from close siblings such as lookup_variant or resolve_identifier, which likely overlap in purpose, so it falls short of a 5.

Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.

Usage Guidelines2/5

Does the description explain when to use this tool, when not to, or what alternatives exist?

No statement of when to use this over lookup_variant, resolve_identifier, or inspect_locus, and no prerequisites or exclusions. The trailing 'Available for: default' is boilerplate that gives an agent no routing signal.

Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.