ClinVar is a freely accessible public archive hosted by NCBI that tracks the relationships between human genetic variants and phenotypes with supporting evidence.

How does this skill handle API access?

The skill provides standardized patterns and best practices for using NCBI's E-utilities (esearch, esummary, efetch) to retrieve variant data programmatically using Python, curl, or Biopython.

Does it support bulk data analysis?

Yes, it provides implementation examples for parsing large XML files and using pandas to analyze tab-delimited summary files from the ClinVar FTP site.

Can I use this for VCF annotation?

Yes, it includes detailed workflows for downloading ClinVar VCFs for GRCh37/GRCh38 and using bcftools to annotate your own variant call sets.

How do I interpret ClinVar star ratings?

The skill explains the 0-4 star review status system, helping you prioritize high-confidence data from expert panels (3 stars) and practice guidelines (4 stars) over single submissions.

ClinVar Database Assistant

Name: ClinVar Database Assistant
Author: Activer007

byActiver007

0•

Data Science & ML

Queries, interprets, and processes human genetic variant data from the NCBI ClinVar archive for genomic research.

This skill empowers Claude to interact with the NCBI ClinVar archive, a critical resource for understanding relationships between human genetic variants and phenotypes. It provides specialized knowledge for querying the database via web and API (E-utilities), interpreting ACMG/AMP clinical significance classifications, and processing bulk genomic data formats like VCF and XML. Whether you are annotating variant call sets, resolving conflicting interpretations using star ratings, or automating data retrieval for genomic medicine pipelines, this skill provides the domain-specific guidance and implementation patterns needed for accurate clinical genetics research.

Key Features

01Advanced querying via NCBI E-utilities API and web interface

02Automated VCF annotation workflows using tools like bcftools

03Guidance on resolving conflicting variant interpretations and tracking updates

04Interpretation of ACMG/AMP clinical significance and star-rated review statuses

050 GitHub stars

06Bulk data processing for VCF, XML, and tab-delimited files

Use Cases

01Automating the annotation of large VCF files with ClinVar pathogenicity data

02Building local genomic databases by parsing monthly ClinVar XML releases

03Identifying high-confidence pathogenic variants for specific genes in clinical research

What are Skills?·How to Install

Install with 🐟 Skill.Fish

npx skillfish add activer007/ordinary-claude-skills clinvar-database

For use in Claude.ai and ChatGPT

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