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calculate_heritability_ldsc

Estimate SNP-heritability from GWAS summary statistics using LD Score regression. Provide summary stats and LD scores to compute heritability.

Instructions

Estimate SNP-heritability using LD Score regression. Requires GWAS summary statistics and LD scores.

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
sumstats_pathYesPath to GWAS summary statistics
ld_scores_pathNoPath to LD scores file
sample_sizeNoGWAS sample size (required if not in sumstats)
Behavior2/5

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

No annotations are provided, so the description carries full burden. It does not disclose behavioral traits like computational cost, side effects, or what the output contains (e.g., heritability estimate, standard error). This is a significant gap for a regression tool.

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 two sentences with no wasted words. The purpose is front-loaded in the first sentence, making it efficient and easy to parse.

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

Completeness2/5

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

Given the tool's complexity (statistical method with dependencies) and no output schema, the description lacks critical context such as what the output is, default behaviors, or how to handle optional parameters like sample_size. This leaves the agent under-informed.

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 coverage is 100%, so the schema already describes each parameter. The description adds no extra semantics beyond what the schema provides, meeting the baseline but not adding value.

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 verb 'Estimate', the resource 'SNP-heritability', and the specific method 'LD Score regression'. It distinguishes itself from sibling tools like calculate_genomic_inflation or calculate_prs by specifying the technique.

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 notes required inputs ('Requires GWAS summary statistics and LD scores'), which gives a prerequisite but no explicit guidance on when to use this tool versus alternatives, such as when to prefer other heritability estimation methods.

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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