vcf_quality_check

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

No annotations are provided, so the description carries full burden. It mentions 'filters variants' indicating mutation, but does not disclose whether the tool modifies the original file, requires specific permissions, or has side effects.

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?

Two concise sentences that efficiently convey the tool's purpose and key filtering metrics, with no redundant information.

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?

The description lacks details on output: does it return a filtered VCF, a report, or both? No output schema exists, so the description should clarify, but it does not.

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?

Input schema has 100% coverage with descriptions for all parameters. The description adds no extra meaning beyond repeating the filtering criteria already in the schema, so baseline 3 applies.

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 'Perform quality control on a VCF file' and specifies the filtering criteria (MAF, missingness, HWE), distinguishing it from sibling tools like 'annotate_snps' or 'calculate_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?

The description implies usage for QC filtering but provides no explicit guidance on when to use this tool versus alternatives, nor does it mention prerequisites or when not to use.

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