Genomics MCP

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get_coverage

Read-only

Compute read depth over a genomic interval from indexed BAM or CRAM files, excluding unmapped, secondary, QC-fail, and duplicate reads by default.

Instructions

Read depth over an interval from indexed BAM/CRAM (default excludes UNMAP, SECONDARY, QCFAIL, DUP, like samtools depth). Available for: bam, cram.

Input Schema

TableJSON Schema

Name	Required	Description
`file`	Yes
`bin_size`	No
`interval`	Yes
`reference`	No
`max_records`	No	Lower the record limit.
`exclude_flags`	No
`min_base_quality`	No
`min_mapping_quality`	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

B3.4/5.0

Behavior4/5

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

Annotations already declare readOnlyHint and openWorldHint, so the safety profile is covered. The description adds real behavioral value by disclosing the default filtering (excludes UNMAP, SECONDARY, QCFAIL, DUP), which explains the opaque exclude_flags=1796 default in the schema. It does not mention failure modes (e.g. index_required) or output shape.

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 tight sentences, front-loading the operation and its scope, with the format constraint appended. No filler, though the samtools reference could have been used to clarify sibling choice instead.

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 needn't be explained, and annotations cover the read-only safety profile. However, for an 8-parameter tool with 13% schema coverage, the description is thin on optional parameters and locus-readiness requirements.

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 13% across 8 parameters. The description accounts for the default exclude_flags behavior but says nothing about bin_size, min_base_quality, min_mapping_quality, max_records, or reference, leaving most parameters undocumented in both places.

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+resource+scope (read depth over an interval from indexed BAM/CRAM) and anchors it with a familiar analogue ('like samtools depth'). It does not differentiate itself from close siblings like get_pileup, get_reads, or get_signal, which an agent would need to choose among.

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: bam, cram' gives a format constraint, so usage is implied rather than spelled out. There is no explicit when-to-use vs get_pileup/get_reads, and no mention of index prerequisites beyond the word 'indexed'.

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