skills.rest
Hung-3008
Hung-3008COMMUNITY
Explore all skills by this author →
GitHub

clinvar-database

Query ClinVar for variant clinical significance and review status from XML, VCF, and tab-delimited datasets.

1|Updated Mar 4, 2026
Search Tags:#genomics#xml#vcf#eutilities#variant-interpretation#ftp#clinvar
One-click install
npx skills add https://github.com/Hung-3008/agusta --skill clinvar-database-hung-3008
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: clinvar-database
Source: https://github.com/Hung-3008/agusta/tree/main/.agents/skills/clinvar-database
Command: npx skills add https://github.com/Hung-3008/agusta --skill clinvar-database-hung-3008

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill includes references (resource) components.

What problem does it solve?

ClinVar aggregates thousands of variant interpretations, making it difficult to access, filter, and integrate this data into research and clinical workflows. This Skill provides a programmatic bridge to search ClinVar data, interpret classifications, and attach clinical context to variants in pipelines.

Core Features & Use Cases

  • Programmatic querying via ClinVar API and FTP datasets to retrieve clinical significance, review status, gene mappings, and conditions.
  • Data integration: annotate variant call sets and reports with ClinVar classifications for streamlined downstream analysis.
  • Use Case: Build a local ClinVar mirror by downloading XML/VCF/RCV data and parsing it for reproducible variant interpretation.

Quick Start

Run a programmatic ClinVar search for BRCA1 pathogenic variants and fetch their summaries for processing.

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 variant clinical significance programmatically?▼

You can query ClinVar programmatically via the E-utilities API to retrieve variant clinical significance, review status, and associated conditions from XML, VCF, and tab-delimited datasets across GRCh37/GRCh38 assemblies.

What is the best way to download bulk ClinVar data for local variant interpretation?▼

The best way to download bulk ClinVar data is via FTP bulk downloads, which provide XML/VCF/RCV datasets to parse and build a local ClinVar mirror for reproducible variant interpretation workflows.

Does ClinVar FTP data work with GRCh37 and GRCh38 assemblies?▼

Yes, ClinVar FTP data and API querying support both GRCh37 and GRCh38 assemblies, allowing researchers and clinicians to retrieve variant clinical significance and associated conditions across both genome builds.

How do I annotate variant call sets with ClinVar classifications?▼

To annotate variant call sets with ClinVar classifications, query the ClinVar API to fetch clinical significance and review status, then integrate this data into your pipelines for streamlined downstream analysis and reporting.

Can I integrate ClinVar XML datasets into a local data mirror using E-utilities?▼

Yes, you can build a local ClinVar mirror by downloading XML/VCF/RCV data via FTP and parsing it for reproducible variant interpretation, while using E-utilities for programmatic querying to attach clinical context to variants.

Why use tab-delimited ClinVar datasets instead of XML for variant interpretation?▼

Tab-delimited ClinVar datasets offer streamlined parsing for bulk data analysis compared to XML, providing clinical significance, review status, and associated conditions in a format easier to integrate into downstream pipelines.

Related Skills

Explore More Data & Analytics Skills→
jimmc414jimmc414
557

clinvar-database

Query NCBI ClinVar for clinical significance of human genetic variants.

Community
Intermediate
jiaxiaojunQAQjiaxiaojunQAQ
75

clinvar-database

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

Community
Intermediate
ovachieverovachiever
52

clinvar-database

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

Community
Advanced
robinbarvaagrobinbarvaag

clinvar-database

Query NCBI ClinVar for genetic variant clinical significance and pathogenicity classifications.

Community
Intermediate