Does it support VCF annotation for bioinformatics pipelines?

Yes, it includes specific workflows for using bcftools to annotate VCF files with ClinVar's clinical significance and condition data.

How do I search for specific genes in ClinVar using this skill?

You can search by gene using the [gene] tag (e.g., BRCA1[gene]) through the web interface or programmatically via the E-utilities esearch API.

Can this skill help process bulk ClinVar data?

Yes, it provides patterns for downloading and parsing multi-GB XML files and VCF records from the NCBI FTP site using Python and command-line tools.

How are conflicting variant interpretations handled?

The skill provides a resolution strategy that prioritizes star ratings (review status), expert panel reviews (ClinGen), and the most recent evidence-based submissions.

Is an API key required for ClinVar access?

While not strictly required, using an NCBI API key increases your rate limit from 3 to 10 requests per second for more efficient data retrieval.

ClinVar Genomic Analysis

Name: ClinVar Genomic Analysis
Author: Zehong-Wang

byZehong-Wang

0•

Data Science & ML

Queries the NCBI ClinVar database to retrieve, interpret, and process human genetic variant classifications and clinical significance.

The ClinVar Database skill enables researchers and developers to interact with NCBI's archive of reports on human genetic variations and their relationship to health. It provides comprehensive guidance on querying the database via web and E-utilities APIs, interpreting ACMG/AMP pathogenicity classifications, and processing bulk genomic data in XML, VCF, and tab-delimited formats. This skill is essential for clinical genetics workflows, variant annotation pipelines, and genomic medicine research where accurate variant interpretation and high-confidence evidence are critical for scientific discovery.

Key Features

01Bulk processing of VCF, XML, and tab-delimited genomic file formats

02Automated VCF annotation workflows for bioinformatics pipelines

03Conflict resolution strategies using review status and star ratings

04Programmatic access via NCBI E-utilities API for automated variant retrieval

05Standardized interpretation of ACMG/AMP pathogenicity classifications

060 GitHub stars

Use Cases

01Building local genomic databases from monthly ClinVar FTP releases

02Identifying high-confidence pathogenic variants for targeted gene research

03Annotating patient VCF files with clinical significance and condition data

What are Skills?·How to Install

Install with 🐟 Skill.Fish

npx skillfish add zehong-wang/kosmos clinvar-database

For use in Claude.ai and ChatGPT

Download Skill