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clinvar-database

Query ClinVar for variant clinical significance via E-utilities and FTP.

75|7|Updated Feb 14, 2026
Search Tags:#data-access#variants#annotation#vcf#clinvar#eutils
One-click install
npx skills add https://github.com/jiaxiaojunQAQ/SkillJect --skill clinvar-database-jiaxiaojunqaq
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: clinvar-database
Source: https://github.com/jiaxiaojunQAQ/SkillJect/tree/main/data/skills_sample/clinvar-database
Command: npx skills add https://github.com/jiaxiaojunQAQ/SkillJect --skill clinvar-database-jiaxiaojunqaq

SYSTEM DOCUMENTATION & REQUIREMENTS

What problem does it solve?

ClinVar provides a centralized resource for clinically significant variant interpretations, enabling researchers and developers to programmatically access, interpret, and integrate variant data into analyses.

Core Features & Use Cases

  • Access ClinVar data via E-utilities (esearch/esummary/efetch) to retrieve variants, clinical significance, and review status.
  • Download and work with FTP datasets (XML, VCF, tab-delimited) for bulk analyses and reproducible pipelines.
  • Annotate variant lists or VCFs with ClinVar classifications to support downstream research and reporting.

Quick Start

Provide a simple, reproducible workflow to query ClinVar for pathogenic BRCA1 variants using esearch and esummary, and fetch full records when needed.

Frequently Asked Questions about clinvar-database

High-intent search queries and answers about installing and using this skill.

FAQPage Schema
How do I query ClinVar variant clinical significance using E-utilities?▼

Query ClinVar variant significance via E-utilities by using esearch to find variants, esummary to retrieve clinical significance and review status, and efetch to pull full records for programmatic analysis.

Can I annotate a VCF file with ClinVar classifications programmatically?▼

Yes, you can annotate VCF files with ClinVar classifications by integrating E-utilities queries or FTP datasets into your genomic pipelines, adding clinical significance and review status to your variant lists.

What is the best way to download ClinVar data for bulk genomic pipeline analysis?▼

Download ClinVar data for bulk analysis via FTP datasets, which provide XML, VCF, and tab-delimited formats suitable for reproducible genomic pipelines and large-scale programmatic processing.

Does this approach support retrieving pathogenic BRCA1 variants from ClinVar?▼

Yes, it supports retrieving pathogenic BRCA1 variants from ClinVar using a reproducible workflow that combines esearch and esummary to filter and fetch specific variant clinical significance records.

What ClinVar data formats are available for tab-delimited programmatic analysis?▼

Available ClinVar data formats for programmatic analysis include XML, VCF, and tab-delimited files, accessible via FTP downloads and E-utilities API endpoints like esearch and efetch.

When should I use E-utilities versus FTP to access ClinVar variant data?▼

Use E-utilities like esearch and esummary for targeted queries retrieving specific variant clinical significance, and use FTP datasets for bulk downloads of XML or VCF files in reproducible genomic pipelines.

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