Genomics MCP

Official

by rewire-bio

Overview Schema Source Related Servers Discussions Admin

Python

Hybrid

compare_samples

Read-only

Compare genotypes or coverage at a genomic interval across files or samples to detect differences.

Instructions

Compare genotypes/coverage at an interval across files or samples. Available for: default.

Input Schema

TableJSON Schema

Name	Required	Description
`files`	Yes
`samples`	No
`interval`	Yes
`reference`	No
`max_records`	No	Lower the record limit.

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

C2.9/5.0

Behavior2/5

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

Annotations already declare readOnlyHint=true and openWorldHint=true, so the safety profile is covered. The description adds no behavioral details beyond the comparison action, such as whether computation is local or remote, permission requirements, or how samples and files interact.

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 description is short and front-loaded with the core action. The trailing 'Available for: default.' is cryptic and does not clearly earn its place, slightly reducing the otherwise efficient structure.

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?

For a complex five-parameter tool with an output schema, the description is too sparse. It omits prerequisites, the relationship between the required files array and optional samples, what exactly is compared, and when to prefer this tool over siblings like get_coverage or get_variants.

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 20%, so the description must compensate. It maps the interval, files, and samples inputs, but leaves reference and max_records unexplained and does not clarify what the sample strings represent or how samples relate to the required files array.

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?

The description states a specific verb (Compare) and resource (genotypes/coverage at an interval across files or samples), making the core action clear. However, it does not distinguish the tool from close siblings like get_coverage, get_variants, or get_pileup, so the agent lacks explicit differentiation.

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?

The description offers no guidance on when to use this tool versus alternatives such as get_coverage or get_variants. The trailing phrase 'Available for: default' does not provide actionable usage context.

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