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tiledbvcf

Stores and retrieves genomic variant calls with TileDB-VCF. Use for indexed single-sample VCF/BCF ingestion, incremental cohorts, region and sample queries, streaming results, allele statistics, QC, and VCF/BCF export locally or through TileDB Cloud.

77

Quality

97%

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SKILL.md
Quality
Evals
Security

Quality

Content

92%Weight 40%Scale 1-5

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

A strong, mature skill body: executable commands with version-specific gotchas, clearly ordered workflow with explicit validation checkpoints, and a clean one-level reference split. The only weakness is mild: version-pin detail and a few caveat sentences overlap with the verification reference and could be tightened.

DimensionReasoningScore

Conciseness

The body is dense and assumes Claude's competence — no library tutorials or concept explanations — with every code block earning its place. It falls short of the lean anchor because time-sensitive pin/version detail (e.g., the azure/capnproto/c-blosc2 pins and repeated 0.40.3/0.14.4 version callouts) and a few defensive caveat sentences ("QC metrics and sparse storage do not establish GWAS readiness") partly duplicate references/verification.md and could be trimmed or relocated.

4 / 5

Actionability

Copy-paste-ready conda, bcftools, CLI, and Python commands cover the common cases, with exact flags, budgets, and gotchas (the `--` separator, `--samples-file` vs comma lists, `dataset_uri` vs `uri`). The cloud snippets are explicitly labeled "Illustrative" with the reason ("requires an accessible registered cohort and a billing namespace"), which is the justified-flexibility case the rubric permits.

5 / 5

Workflow Clarity

Sections are sequenced as a pipeline (install → prepare → create → ingest → query → export → stats/QC → cloud) with explicit validation checkpoints: "Validate a small known interval and a round-trip export before scaling", round-trip comparison of sample IDs/contigs/record counts, "Check expected artifacts and sample counts as well as the exit code", and "track that graph to terminal success and verify ingested samples before claiming completion". Recovery guidance exists ("resume=True supports interrupted ingestion"), matching the validation-plus-checkpoint anchor.

5 / 5

Progressive Disclosure

The single bundle file, references/verification.md, exists and is clearly signaled from the body twice ("See [installation and verification notes](references/verification.md)" and under Official references), one level deep. The split is appropriate: the body keeps actionable guidance while verification provenance (environment solves, contract checks) lives in the reference, making navigation easy.

5 / 5

Total

19

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20

Passed

Description

100%Weight 40%Scale 1-5

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

The description is exemplary: third-person, concise, and specific, with a clear what and an explicit 'Use for' trigger clause enumerating the tool's real capabilities. Trigger terms match what genomics users would naturally say, and the niche is unambiguous.

DimensionReasoningScore

Specificity

"Stores and retrieves genomic variant calls" plus a list of concrete actions — "indexed single-sample VCF/BCF ingestion, incremental cohorts, region and sample queries, streaming results, allele statistics, QC, and VCF/BCF export locally or through TileDB Cloud" — comprehensively covers the tool's surface. Matches the anchor for multiple specific concrete actions with comprehensive coverage, exceeding the 4 anchor's 'minor gaps'.

5 / 5

Completeness

The what is explicit ("Stores and retrieves genomic variant calls with TileDB-VCF") and the when is an explicit trigger clause ("Use for indexed single-sample VCF/BCF ingestion, incremental cohorts...") with concrete trigger phrases. Both are clearly and explicitly answered, matching the top anchor rather than the 4 anchor's 'when could be more specific'.

5 / 5

Trigger Term Quality

Natural domain terms users would actually say are all present: "VCF", "BCF", "genomic variant calls", "ingestion", "cohorts", "region and sample queries", "allele statistics", "QC", "export", "TileDB Cloud". Coverage includes file formats (VCF/BCF), domain synonyms, and the cloud variant, fitting the comprehensive-synonyms anchor.

5 / 5

Distinctiveness Conflict Risk

"TileDB-VCF" with genomic-variant triggers (VCF/BCF ingestion, cohorts, allele statistics) carves a clear niche distinct from generic file or data skills; the tool name and domain-specific triggers make wrong-skill conflicts unlikely.

5 / 5

Total

20

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20

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.

Validation — 16 / 16 Passed

Validation for skill structure

No warnings or errors.

Repository

K-Dense-AI/scientific-agent-skills

Path

skills/tiledbvcf/SKILL.md

Reviewed

Table of Contents

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