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rewire-bio

genomics-mcp

Official
by rewire-bio

normalize_variant

Read-only

Normalize VCF-style, HGVS, or rsID variants to a standard representation on an explicit genome assembly, making them comparable and analysis-ready.

Instructions

Normalize a variant (VCF-style, HGVS or rsID) on an explicit assembly with a trace. Not implemented in this build: returns error code 'unsupported' (E8).

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
hgvsNo
rsidNo
sourcesNoSource names; default all available.
variantNo
assemblyNo
referenceNo

Output Schema

TableJSON Schema
NameRequiredDescriptionDefault
dataNo
errorNoSet when status is error.
errorsNoPer-source failures in partial results.
limitsNo
statusYes
warningsNo
operationYes
provenanceNo
truncationNo
source_statusNo
schema_versionNo1

Schema Changelog

Changes observed during successful MCP inspections.

  1. First observedv0.1.0

TDQS

A4.1/5.0
Behavior4/5

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

Beyond the readOnlyHint and openWorldHint annotations, the description discloses the most important runtime behavior: the feature is a stub that returns 'unsupported' (E8). This gives the agent the critical failure-mode context needed to avoid invoking it. The meaning of 'trace' is left vague, but no contradiction exists.

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

Conciseness5/5

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

Two short sentences, both purposeful: the first states the operation and constraints, the second states the critical unsupported status. There is no filler, repetition, or unnecessary reproduction of schema fields.

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

Completeness3/5

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

The unsupported notice is the most important contextual fact and is present, so an agent knows not to expect a working result. However, the description leaves parameter selection and the meaning of 'trace' unexplained, and does not point to an alternative tool, so the agent is not fully equipped to route to a working normalization path.

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 description must compensate. It usefully maps 'VCF-style, HGVS or rsID' to the variant/hgvs/rsid parameters and emphasizes an explicit assembly, but it does not address the reference or sources parameters, nor the expected mutual exclusivity of the three input modes. This is helpful but incomplete for safe invocation.

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

Purpose5/5

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

The description states a specific action ('Normalize a variant'), enumerates accepted input forms (VCF-style, HGVS, rsID), and adds a distinctive condition ('explicit assembly', 'with a trace'). This is enough to set it apart from sibling lookup/resolve tools without requiring schema inspection.

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

Usage Guidelines4/5

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

It explicitly says the tool is not implemented in this build and returns error code E8, which is a clear when-not-to-use signal. It does not name a fallback alternative such as lookup_variant or resolve_identifier, so it stops short of full routing guidance.

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