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clinvar-database

Query ClinVar variant data via E-utilities and FTP bulk downloads.

7|Updated Jan 27, 2026
Search Tags:#genomics#variants#vcf#ftp#clinvar#eutils#clinical-significance
One-click install
npx skills add https://github.com/wsxwj123/opencode-skills-backup --skill clinvar-database-wsxwj123
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: clinvar-database
Source: https://github.com/wsxwj123/opencode-skills-backup/tree/main/clinvar-database
Command: npx skills add https://github.com/wsxwj123/opencode-skills-backup --skill clinvar-database-wsxwj123

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill includes references (resource) components.

What problem does it solve?

ClinVar provides a comprehensive, programmatic path to access variant interpretations, enabling researchers to search, retrieve, and interpret clinical significance data for genomic variants without manual data wrangling.

Core Features & Use Cases

  • Programmatic access to ClinVar via E-utilities for gene/variant searches and record summaries
  • Bulk data retrieval through FTP (VCV/RCV/SCV, VCF, and tab-delimited formats) for reproducible pipelines
  • Annotation and analysis workflows: filter by clinical significance, review status, and disease associations; integrate with downstream pipelines and research studies
  • Use Case: Build a local ClinVar catalog of pathogenic BRCA1/BRCA2 variants and annotate sample VCFs with CLNSIG

Quick Start

Run a quick query for BRCA1 pathogenic variants using eutils and export summaries to JSON.

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 for pathogenic variants and export the results?▼

Query ClinVar for pathogenic variants using E-utilities to search gene or variant records and export summaries to JSON for local data analysis and reproducible research workflows.

Can I download bulk ClinVar variant data in VCF format via FTP?▼

Yes, bulk ClinVar variant data is available via FTP in VCF, XML, and tab-delimited formats, enabling you to build local catalogs of VCV, RCV, and SCV records for reproducible pipelines.

How do I annotate a sample VCF with ClinVar clinical significance?▼

Annotate sample VCFs with CLNSIG by retrieving ClinVar variant data through E-utilities or FTP, then filtering records by clinical significance and disease associations for interpretation.

What formats are supported for ClinVar bulk data retrieval?▼

ClinVar bulk data retrieval supports VCF, XML, and tab-delimited formats, providing structured outputs that integrate with downstream genomics analysis pipelines and variant research studies.

Does this approach require manual data wrangling to interpret genomic variants?▼

No, programmatic access to ClinVar provides structured outputs for variant interpretation, enabling researchers to search, retrieve, and interpret clinical significance data without manual data wrangling.

How do I filter ClinVar variants by review status and disease associations?▼

Filter ClinVar variants by review status and disease associations during local data analysis after retrieving records via E-utilities or FTP, enabling targeted annotation workflows for clinical-research studies.

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