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by net.genebe
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liftover_coordinate

Read-onlyIdempotent

Convert a genomic position, interval or variant between genome builds (hg19, hg38, t2t).

Check status: RESOLVED means one result, AMBIGUOUS means several candidates, anything else means it could not be mapped (see errors). For variants, ref/alt are rebuilt against the target reference and warnings such as REF_MISMATCH may apply.

Tool call template

Replace each placeholder with a value matching the input schema. Only required parameters are included; add optional parameters as needed.

{
  "id": 1,
  "jsonrpc": "2.0",
  "method": "tools/call",
  "params": {
    "arguments": {
      "query": "<query>",
      "from_genome": "<from_genome>",
      "to_genome": "<to_genome>"
    },
    "name": "liftover_coordinate"
  }
}

Input Schema

NameRequiredDescriptionDefault
queryYesA position ('chr8:141310715'), an interval ('chr8:141310715-141310716') or a variant ('chr2-23423-A-C', HGVS, rsID).
to_genomeYesGenome build to convert to.
from_genomeYesGenome build of the input.

Output Schema

NameRequiredDescriptionDefault
inputYes
errorsYes
statusYesRESOLVED, AMBIGUOUS, UNRESOLVED, INVALID, NOT_RECOGNIZED or UNSUPPORTED
warningsYes
to_genomeYes
candidatesYes
from_genomeYes

Schema Changelog

Changes observed during successful MCP inspections.

  1. First observed

TDQS

A3.7/5.0
Behavior4/5

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

Annotations already declare readOnly, idempotent, openWorld and non-destructive, so the safety profile is covered. The description adds real behavioral context beyond that: the RESOLVED/AMBIGUOUS/other status contract, the possibility of unmappable coordinates surfaced via errors, and that variant ref/alt are rebuilt against the target reference with warnings like REF_MISMATCH.

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

Conciseness4/5

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

The purpose sentence is front-loaded and the second paragraph is dedicated to result interpretation, so every sentence earns its place. Slightly dense in the status sentence, but no filler.

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

Completeness4/5

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

With an output schema present, the description needn't enumerate return fields, and it correctly focuses on how to read status and warnings. The remaining gap is sibling disambiguation against `convert_variant`, which an agent would still have to resolve by opening both schemas.

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 100% and each parameter carries its own description, so the schema does the heavy lifting. The description adds only marginal signal, reiterating the build names and noting variant handling, without extra format or edge-case detail for `query` beyond what the schema lists.

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 specific verb (convert) and resource (genomic position, interval or variant) plus the supported builds (hg19, hg38, t2t). It is clear on its own, but it never distinguishes itself from the sibling `convert_variant`, which plausibly overlaps for the variant case — the one ambiguity that matters most here.

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

Usage Guidelines3/5

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

Usage is only implied by the purpose statement; there is no explicit when-to-use/when-not and no routing to or away from `convert_variant` or `annotate_variant`. What guidance exists is about interpreting output (status values, errors), not about tool selection.

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

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