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genomic-coordinates

Convert genomic intervals between coordinate conventions, normalise and compare variant representations, and detect assembly or contig-naming mismatches before they corrupt an analysis. Use whenever coordinates cross a format, tool, or assembly boundary - converting between BED, GFF/GTF, VCF, SAM/BAM, WIG, PSL, genePred, Picard interval_list, or region strings; reconciling 0-based half-open with 1-based inclusive; left-aligning or trimming indels; checking whether two variant records describe the same change; mapping genomic to transcript, CDS, or protein positions; auditing a BED/GTF/VCF for convention violations; or diagnosing GRCh37 vs hg19 vs GRCh38 vs T2T, chr-prefix, and liftover problems. Triggers include "off by one", "0-based", "1-based", "half-open", "coordinate system", "left-align", "normalize variant", "bcftools norm", "chr prefix", "wrong genome build", "liftover", "REF mismatch", and "HGVS".

80

Quality

100%

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SKILL.md
Quality
Evals
Security

Quality

Content

100%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 well-structured skill body that is lean, executable, and rich in validation checkpoints, with detail correctly deferred to four real reference files and helper scripts. It is a strong example of progressive disclosure for a non-trivial multi-task domain.

DimensionReasoningScore

Conciseness

Lean body that assumes Claude's genomics knowledge, avoids explaining what BED/VCF are, and lets every section earn its place; no padded introductory prose.

5 / 5

Actionability

Copy-paste-ready bash commands with concrete arguments and example output tables for convert_coords.py, normalize_variant.py, check_contigs.py, and audit_intervals.py cover the common cases.

5 / 5

Workflow Clarity

Explicit validation checkpoints throughout - REF checked against FASTA first, MISMATCH halts and routes to check_contigs.py, --split before normalising, exit code 1 as a CI gate - with clear error-recovery feedback loops for batch/destructive operations.

5 / 5

Progressive Disclosure

Clear overview body with four well-signaled one-level-deep references (format-conventions, variant-representation, reference-builds, transcript-coordinates), all of which exist as real files, with detailed content appropriately split out of the main file.

5 / 5

Total

20

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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.

An exceptionally specific and complete description that clearly states capabilities, use conditions, and trigger keywords in third-person voice. It risks slight verbosity but every clause maps to a concrete capability or trigger.

DimensionReasoningScore

Specificity

Lists multiple concrete actions - converting intervals across BED/GFF/VCF/SAM formats, normalising and comparing variants, left-aligning indels, auditing files, and mapping genomic to transcript positions - covering the domain comprehensively.

5 / 5

Completeness

Explicitly answers 'what' (convert/normalise/compare/audit coordinate and variant representations) and 'when' via a concrete 'Use whenever coordinates cross a format, tool, or assembly boundary' clause with enumerated cases.

5 / 5

Trigger Term Quality

Provides an explicit trigger list with natural user phrases ('off by one', 'wrong genome build', 'liftover') plus tool names (bcftools norm) and synonyms, giving comprehensive coverage.

5 / 5

Distinctiveness Conflict Risk

Occupies a clear niche (genomic coordinate conventions and assembly mismatches) with domain-specific triggers that are unlikely to fire for unrelated skills.

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.

Validation16 / 16 Passed

Validation for skill structure

No warnings or errors.

Repository
K-Dense-AI/scientific-agent-skills
Reviewed

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