qc_call_rate

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

With no annotations provided, the description carries the full burden. It transparently describes outputs (two CSV files), return summary contents, and the effect of the method parameter (full export vs. estimation). It does not mention authorization or side effects beyond file writing, but given the absence of annotations, this is sufficient.

Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.

Is the description appropriately sized, front-loaded, and free of redundancy?

The description is a single paragraph but well-structured: purpose first, then outputs, then parameter clarifications. It is efficient with no wasted words, though slightly dense. Could benefit from bullet points for readability, but still concise.

Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.

Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?

Given 7 parameters with full schema coverage and an output schema, the description covers all necessary aspects: tool purpose, output files, parameter explanations, and usage advice. It is complete for an agent to invoke correctly.

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

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

Schema coverage is 100%, so baseline is 3. The description adds significant value beyond the schema: it explains the source of variant_set_db_id (from list_content), clarifies the allelematrix method for large sets, specifies the 1-based coordinate system for region, and describes the max_markers cap. This helps the agent select appropriate parameters.

Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.

Does the description clearly state what the tool does and how it differs from similar tools?

The description clearly states the tool performs per-sample and per-marker call rate QC, including flagging samples/markers below thresholds, writing specific output files, and returning a summary. It distinguishes itself from sibling QC tools like qc_duplicate_accessions or qc_maf_filter by its specific focus on call rate/missingness.

Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.

Does the description explain when to use this tool, when not to, or what alternatives exist?

Provides explicit guidance on when to use alternative methods (e.g., 'For large production sets pass method="allelematrix"') and explains the region parameter restriction. However, it does not explicitly state when not to use this tool compared to other QC tools, nor does it list prerequisites.

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