Genomics MCP

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get_variants

Read-only

Extract variant records and optional genotypes overlapping a genomic interval from VCF or BCF files, with sample, PASS, and record-limit filters.

Instructions

Variant records and optional genotypes overlapping an interval (VCF/BCF). Available for: bcf, vcf.

Input Schema

TableJSON Schema

Name	Required	Description
`file`	Yes
`samples`	No
`interval`	Yes
`pass_only`	No
`max_records`	No	Lower the record limit.
`include_genotypes`	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

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 safety and external-access behavior are covered. The description adds format availability and that genotypes are optional, but omits behavioral details like pagination, record limits, or required file readiness.

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, front-loaded sentences with no filler. The core operation is stated first, followed by a concise format constraint.

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?

Although an output schema exists and reduces the need to explain return values, the description is too sparse for a 6-parameter tool with low schema coverage. It omits guidance on alternatives, filtering, and the roles of most optional parameters, so an agent would need to inspect the schema heavily to invoke it correctly.

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 17%, so the description must carry more weight but does not. It mentions interval and optional genotypes, but says nothing about samples, pass_only, max_records, or include_genotypes, leaving most parameters semantically opaque.

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 clearly identifies the resource (variant records), scope (overlapping an interval), and supported formats (VCF/BCF). It distinguishes itself from most siblings like get_sequence and get_features, though it does not explicitly contrast with closely related tools such as lookup_variant or normalize_variant.

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?

The phrase 'Available for: bcf, vcf' gives a format eligibility constraint, which implies when the tool can be used. However, it provides no guidance on when to choose this over sibling tools like lookup_variant or get_features, leaving selection to inference.

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