Genomics MCP

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get_signal

Read-only

Extract signal values or binned summaries over a genomic interval from bigWig files to analyze coverage and signal profiles.

Instructions

Signal values or binned summaries over an interval from bigWig. Available for: bigwig.

Input Schema

TableJSON Schema

Name	Required	Description	Default
`bins`	No
`file`	Yes
`summary`	No		mean
`interval`	Yes
`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

B3.2/5.0

Behavior3/5

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 the bigWig-only constraint and the binned-summary capability, but says nothing about aggregation defaults, record limits, or what the returned signal looks like.

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?

Two short sentences, front-loaded with the core capability. No filler, though the 'Available for: bigwig' line is terse enough that it could carry slightly more useful constraint detail.

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?

An output schema exists, so return values need no explanation, and annotations cover safety. However, with 20% schema coverage the thin parameter documentation leaves meaningful gaps for bins, summary, and max_records semantics.

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

Parameters2/5

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

Schema description coverage is only 20% across 5 parameters, so the description must compensate and largely does not. It alludes to 'binned summaries over an interval' (bins, interval) but leaves the summary enum options (mean/min/max/coverage/std/sum) and max_records unexplained.

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 and resource: retrieving signal values or binned summaries over an interval, scoped to bigWig files. An agent can distinguish this from siblings like get_coverage or get_pileup by the 'signal values from bigWig' framing, though those alternatives are never named explicitly.

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?

'Available for: bigwig' implies the precondition (file must be bigWig format), which is useful, but there is no explicit when-to-use versus get_coverage, get_pileup, or get_reads. Usage is only weakly implied.

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