clinvar-database

Query NCBI ClinVar for variant clinical significance. Search by gene/position, interpret pathogenicity classifications, access via E-utilities API or FTP, annotate VCFs, for genomic medicine.

1.15x

Quality

83%

Does it follow best practices?

Impact

88%

1.15x

Average score across 3 eval scenarios

Securityby

Advisory

Suggest reviewing before use

Evaluation results

78%

22%

ClinVar Variant Research Tool

ClinVar E-utilities API best practices

Criteria

Without context

With context

Email identification

100%

API key parameter

Exponential backoff

100%

usehistory for large results

esummary version=2.0

100%

Batch ID retrieval

100%

Exclude conflicting interpretations

70%

100%

Review status filtering

12%

50%

Access date recorded

100%

Correct API pipeline order

100%

Three gene reports produced

100%

14%

Clinical VCF Annotation Workflow

VCF annotation with ClinVar and bcftools

Criteria

Without context

With context

Correct genome build

100%

Index file downloaded

100%

bcftools annotate -a flag

100%

bcftools -c columns flag

100%

Pathogenic filter command

100%

Review status annotation

100%

Conflicting interpretations flagged

100%

VCF size limitation documented

100%

ClinVar version/date documented

50%

100%

Large file cleanup

100%

Output files produced

100%

86%

-2%

Hereditary Cardiac Disease Variant Analysis

Bulk data format selection and reproducible analysis

Criteria

Without context

With context

Tab-delimited format chosen

100%

Monthly release URL

62%

100%

pandas sep and compression

80%

Conflicting variants counted separately

100%

High-confidence filter

30%

VUS reported separately

100%

75%

Access date in report

100%

Data source documented

100%

All four genes covered

100%

Large file cleanup

100%

Output file produced

100%

Repository: K-Dense-AI/claude-scientific-skills
Commit: 71add64

Evaluated: 27 days ago
Agent: Claude Code
Model: Claude Sonnet 4.6

Table of Contents

ClinVar Variant Research Tool Clinical VCF Annotation Workflow Hereditary Cardiac Disease Variant Analysis

Is this your skill?

If you maintain this skill, you can claim it as your own. Once claimed, you can manage eval scenarios, bundle related skills, attach documentation or rules, and ensure cross-agent compatibility.