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diversity_kinship

Computes a genomic relationship matrix from genotyping data to identify related sample pairs and estimate inbreeding levels.

Instructions

VanRaden genomic relationship (kinship) matrix.

Computes G = ZZ'/(2 Σp(1-p)) from alt dosage. Writes the full matrix as kinship_matrix.csv (samples × samples) and reports the most-related pairs and the diagonal (self-relationship / inbreeding) range. For large sets pass method="allelematrix" + max_markers to avoid a full VCF export.

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
methodNoGenotype source: 'vcf' (full export, cached) or 'allelematrix' (paged, server-side subset).vcf
regionNoRestrict analysis to a genomic window: 'chrom' or 'chrom:start-end' (1-based).
top_pairsNoHow many most-related sample pairs to report.
output_dirNoDirectory for the output CSV(s) (default ./gigwa_results/<module>/).
max_markersNoCap the number of markers analysed (evenly-spaced subsample); omit to use all.
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?

With no annotations, the description carries the full burden. It discloses outputs (writes CSV, reports pairs and diagonal) and offers a performance hint for large sets. However, it does not mention potential mutation (appears read-only), required permissions, or resource consumption, leaving gaps.

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

Conciseness5/5

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

The description is concise (4 sentences, ~83 words), front-loaded with the core purpose, and every sentence earns its place (formula, output details, performance guidance). No fluff or repetition.

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 moderate complexity, schema coverage, and output schema existence, the description covers essential aspects: formula, output files, and performance hint. It does not explain all parameters in depth (schema covers them) but is largely complete for an informed selection.

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%, setting baseline at 3. The description adds value by explaining the formula context and explicitly advising when to use method='allelematrix' with max_markers, which enriches the semantic understanding beyond the schema's 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 the tool computes a VanRaden genomic relationship (kinship) matrix, specifying the formula and outputs (csv, related pairs, diagonal range). This distinguishes it from sibling diversity tools (e.g., diversity_pca, diversity_structure) which address different analyses.

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?

The description implies the tool is for kinship/relationship analysis but does not explicitly compare to siblings or state when not to use it. It provides guidance on using method='allelematrix' for large sets, but lacks exclusions or alternatives for other diversity analyses.

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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