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tooluniverse-gwas-finemapping

Statistical fine-mapping of GWAS loci using credible sets (SuSiE, FINEMAP) and locus-to-gene scoring (Open Targets L2G). Identifies likely causal variants and target genes — distinct from positional 'nearest gene' which is often wrong. Use for prioritizing causal variants at GWAS hits, comparing fine-mapping methods, and converting lead SNPs to target genes.

64

Quality

75%

Does it follow best practices?

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SecuritybySnyk

Low

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tessl review fix ./plugin/skills/tooluniverse-gwas-finemapping/SKILL.md
SKILL.md
Quality
Evals
Security

Quality

Content

50%

Reviews the quality of instructions and guidance provided to agents. Good implementation is clear, handles edge cases, and produces reliable results.

The content is well-structured and domain-accurate with a genuinely useful reasoning framework, but it underperforms on token efficiency (teaching genetics Claude already knows), provides no executable code despite mandating computation, and keeps everything in a single monolithic file. It reads more as a textbook chapter than a lean operational skill.

Suggestions

Cut the Overview and 'Key Concepts' explanations of GWAS, LD, credible sets, and posterior probability — assume Claude's competence and keep only the skill-specific reasoning framework and thresholds.

Add at least one concrete, copy-paste-ready Python example invoking the named Open Targets / GWAS Catalog tools, since the skill mandates 'COMPUTE, DON'T DESCRIBE' but shows no code.

Move the tool reference list, FAQ, and output-interpretation bands into one-level-deep reference files (e.g. TOOLS.md, INTERPRETATION.md) and link them from the overview to reduce the monolithic body.

DimensionReasoningScore

Conciseness

The body is mostly efficient, but the Overview and 'Key Concepts' sections re-explain GWAS, linkage disequilibrium, credible sets, posterior probability, and L2G — concepts a capable model already knows — which is padding the rubric penalizes.

2 / 3

Actionability

Concrete tool names and PP/L2G thresholds are given, but despite the 'COMPUTE, DON'T DESCRIBE' mandate there is no executable code anywhere — tool calls appear only as prose names with no example invocations or arguments.

2 / 3

Workflow Clarity

The 5-step reasoning framework is clearly sequenced with conditional logic at each step, but there are no explicit validation checkpoints, feedback loops, or checklists — the decision points are implicit rather than enforced.

2 / 3

Progressive Disclosure

The ~170-line body is monolithic with no bundle/reference files; content that could be split out (the tool reference list, FAQ, and output-interpretation bands) is inline rather than one level deep in signaled reference files.

2 / 3

Total

8

/

12

Passed

Description

100%

Based on the skill's description, can an agent find and select it at the right time? Clear, specific descriptions lead to better discovery.

A strong, third-person description that concretely names capabilities, gives explicit use-when triggers, and stakes out a distinct niche with natural domain vocabulary. The only minor risk is overlap with sibling skills (eqtl-colocalization, gene-prioritization), but the description mitigates this by naming methods and contrasting with nearest-gene heuristics.

DimensionReasoningScore

Specificity

Lists multiple concrete actions — 'Statistical fine-mapping of GWAS loci using credible sets (SuSiE, FINEMAP)', 'locus-to-gene scoring (Open Targets L2G)', and 'prioritizing causal variants…comparing fine-mapping methods…converting lead SNPs to target genes'.

3 / 3

Completeness

Explicitly answers both what it does and when to use it via the 'Use for prioritizing causal variants at GWAS hits, comparing fine-mapping methods, and converting lead SNPs to target genes' clause.

3 / 3

Trigger Term Quality

Uses natural domain terms a researcher would actually say — 'fine-mapping', 'GWAS', 'causal variants', 'lead SNPs', 'target genes' — with good coverage and no over-reliance on jargon.

3 / 3

Distinctiveness Conflict Risk

Carves a clear niche (credible-set fine-mapping + L2G) and explicitly distinguishes itself from positional 'nearest gene' approaches, with triggers unlikely to fire for adjacent skills.

3 / 3

Total

12

/

12

Passed

Validation

100%

Checks the skill against the spec for correct structure and formatting. All validation checks must pass before discovery and implementation can be scored.

Validation16 / 16 Passed

Validation for skill structure

No warnings or errors.

Repository
mims-harvard/ToolUniverse
Reviewed

Table of Contents

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