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export_genotypes

Export a variant set to a file in VCF, PLINK, or Flapjack format. Specify the variant set database ID and output path to download the genotyping data.

Instructions

Export a variant set to a file in the given format.

format is one of Gigwa's export formats. Which are available depends on the Gigwa build — VCF (default), PLINK and FLAPJACK are commonly supported; others (HAPMAP, DARWIN, …) may not be, in which case the tool reports the formats this instance actually offers. The export runs server-side and is streamed to output_path. For large sets this can take a while; raise timeout (seconds).

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
formatNoExport format: VCF, PLINK or Flapjack (availability varies by Gigwa build).VCF
timeoutNoMaximum seconds to wait for the export to complete.
output_pathYesDestination file path for the export.
variant_set_db_idYesBrAPI variantSetDbId identifying the run (MODULE§project§run); from list_variant_sets / list_content.

Output Schema

TableJSON Schema
NameRequiredDescriptionDefault
resultYes
Behavior3/5

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

The description discloses that the export runs server-side, is streamed to output_path, and can be time-consuming. It also mentions that unavailable formats are reported. However, it lacks details about permissions, data volume limits, overwrite behavior, or error handling. With no annotations, the description bears full burden; it provides useful but incomplete transparency.

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?

The description is two paragraphs: a concise purpose statement followed by a informative block about format and timeout. It avoids fluff and is well-structured, though some repetition with schema descriptions exists (e.g., format default). Overall, it is appropriately sized and front-loaded.

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

Completeness4/5

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

Given the tool's complexity (export, server-side, streaming), the description covers purpose, format variability, timeout, and streaming behavior. An output schema exists, so return values are documented elsewhere. The description is complete enough for a 4-parameter tool with full schema coverage.

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

Parameters4/5

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

Schema coverage is 100%, baseline 3. The description adds value beyond the schema by explaining format availability (common formats, build-dependent), that the tool reports available formats, and that timeout is in seconds. This provides context not present in the schema descriptions.

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

Purpose5/5

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

The description clearly states 'Export a variant set to a file in the given format', specifying the verb (export), resource (variant set), and output (file). Among sibling tools (import, qc, diversity, etc.), export_genotypes is unique in its function, so it is easily distinguished.

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

Usage Guidelines4/5

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

The description provides context for when to use the tool: to export a variant set to a file. It mentions that format availability depends on the Gigwa build and that export can take a while, suggesting raising timeout. However, it does not explicitly state when not to use it or list direct alternatives among siblings, but the guidance is adequate.

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

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