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clinvar-database

Query ClinVar variant classifications and evidence via E-utilities and FTP.

1|Updated Mar 19, 2026
Search Tags:#python#genomics#vcf#eutilities#variant-interpretation#ftp#clinvar
One-click install
npx skills add https://github.com/JosephWoodall/noosphere --skill clinvar-database-josephwoodall
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: clinvar-database
Source: https://github.com/JosephWoodall/noosphere/tree/main/.agent/skills/clinvar-database
Command: npx skills add https://github.com/JosephWoodall/noosphere --skill clinvar-database-josephwoodall

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill includes references (resource) components.

What problem does it solve?

ClinVar is a central resource for variant interpretations; this skill provides programmatic access to search, retrieve, and interpret ClinVar records, enabling researchers to build pipelines that annotate variants, assess clinical significance, and track review status at scale.

Core Features & Use Cases

  • Programmatic access to ClinVar via E-utilities, Entrez Direct, and FTP bulk downloads for XML, VCF, and tab-delimited formats.
  • Variant search and interpretation by gene, disorder, or CLNSIG, with retrieval of summaries and linked evidence.
  • Data integration and annotation: annotate VCFs with CLNSIG, CLNREVSTAT, and related fields; cross-reference PubMed and ClinGen resources.
  • Bulk data workflows: download monthly releases and incremental updates for reproducible analyses; build local ClinVar databases.
  • Use cases: implement pipelines that extract pathogenic variants, filter by review status, and drive research reports or clinical-genomics studies.

Quick Start

Query ClinVar for pathogenic BRCA1 variants and retrieve summaries for downstream annotation.

Frequently Asked Questions about clinvar-database

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

FAQPage Schema
How do I annotate VCF files with ClinVar variant classifications programmatically?▼

You can annotate VCF files with ClinVar variant classifications by querying CLNSIG, CLNREVSTAT, and related metadata fields to append clinical significance and review status directly to your variant records.

What is the best way to download bulk ClinVar data for a local database?▼

Downloading bulk ClinVar data for a local database is best handled via FTP, which provides monthly releases and incremental updates in XML, VCF, and tab-delimited formats for reproducible analyses.

Can I search ClinVar for pathogenic variants by gene or disorder using E-utilities?▼

Yes, you can search ClinVar for pathogenic variants by gene, disorder, or clinical significance using E-utilities and Entrez Direct to retrieve summaries and linked evidence programmatically.

How does ClinVar review status help filter variants in genomics pipelines?▼

ClinVar review status helps filter variants in genomics pipelines by providing the CLNREVSTAT field, allowing you to assess the confidence level of clinical interpretations and prioritize high-confidence pathogenic calls.

Does this ClinVar query workflow support cross-referencing PubMed and ClinGen resources?▼

Yes, the workflow supports cross-referencing PubMed and ClinGen resources, enabling you to validate ClinVar variant interpretations against linked literature and clinical guidelines during data integration.

What formats are available for retrieving ClinVar summary records?▼

ClinVar summary records are available for retrieval in XML, VCF, and tab-delimited formats, allowing seamless integration into downstream annotation pipelines and genomics research workflows.

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