Genomics MCP

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get_reads

Read-only

Retrieve alignments overlapping a genomic interval from indexed BAM/CRAM files, applying flag and mapping-quality filters; provide a matching reference for CRAM unless self-contained.

Instructions

Alignments overlapping an interval from indexed BAM/CRAM. Flag filters follow samtools -f/-F. CRAM needs a matching reference unless self-contained. Available for: bam, cram.

Input Schema

TableJSON Schema

Name	Required	Description
`file`	Yes
`interval`	Yes
`reference`	No
`max_records`	No	Lower the record limit.
`exclude_flags`	No
`require_flags`	No
`include_sequence`	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

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 usefully adds that CRAM requires a matching reference unless self-contained and that flag filters mirror samtools -f/-F, but says nothing about record limits, error behavior, or paging.

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?

Three tight sentences, front-loaded with the core operation before the format constraint and the CRAM caveat. No filler, though the samtools flag note could be folded into the flag parameters rather than the top-level description.

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?

For an 8-parameter, read-only tool with an output schema, the description covers the operation, applicability, and the key CRAM prerequisite. Given the very low schema coverage it still leaves several parameters and any limit/error semantics unexplained, so it is adequate but not complete.

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 13%, so the description must carry weight: it does explain the flag semantics (mapping to exclude_flags/require_flags) and the reference requirement. But max_records, include_sequence, and min_mapping_quality get no mention, leaving part of the parameter set undocumented.

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?

Specifies the verb+resource ('alignments overlapping an interval') and the applicable formats ('indexed BAM/CRAM'), which cleanly distinguishes it from get_sequence, get_features, and get_pileup. It never names a sibling explicitly, so it stops just short of a 5.

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' states applicability by file type, and the CRAM reference caveat is a genuine prerequisite. However, there is no guidance on when to choose this over get_pileup, get_coverage, or get_variants, leaving alternatives to inference.

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