How does it handle conflicting variant interpretations?

The skill outlines a resolution strategy based on review status (star ratings), submission dates, and evidence levels to help users evaluate conflicting data points.

Is an API key required for ClinVar access?

While not required for basic use, the skill recommends using an NCBI API key to increase rate limits from 3 to 10 requests per second for automated tasks.

How does this skill access ClinVar data?

It provides implementation patterns for using NCBI's E-utilities API for programmatic access, web queries for manual search, and bulk downloads from the ClinVar FTP site.

Can it help with VCF annotation?

Yes, it includes specific workflows for using tools like bcftools to annotate variant call sets with ClinVar clinical significance and metadata.

Which genome builds are supported?

The skill provides guidance for accessing data for both GRCh37 and GRCh38 builds, ensuring compatibility with modern genomic pipelines.

ClinVar Database Integration

Name: ClinVar Database Integration
Author: pur3v4d3r

bypur3v4d3r

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Data Science & ML

Queries and interprets NCBI ClinVar data to evaluate genetic variant pathogenicity and clinical significance for genomic medicine.

About

The ClinVar Database skill enables seamless interaction with NCBI’s public archive of human genetic variants and their relationship to human health. It provides specialized guidance for querying variants by gene or condition, interpreting ACMG/AMP pathogenicity classifications, and processing bulk data via E-utilities API or FTP. This skill is essential for bioinformaticians and researchers needing to annotate VCF files, resolve conflicting interpretations, and automate the retrieval of standardized clinical significance data within their genomic pipelines.

Key Features

Interpret ACMG/AMP clinical significance classifications
Query ClinVar via E-utilities API and web interface
Cross-reference variants with review status and star ratings
1 GitHub stars
Bulk data processing for XML, VCF, and tab-delimited formats
Automate variant call set (VCF) annotation with clinical metadata

Use Cases

Annotating VCF files with pathogenicity data for clinical research pipelines
Identifying high-confidence pathogenic variants in specific genes like BRCA1 or CFTR
Building and updating local ClinVar databases via FTP automation

About

Key Features

Interpret ACMG/AMP clinical significance classifications
Query ClinVar via E-utilities API and web interface
Cross-reference variants with review status and star ratings
1 GitHub stars
Bulk data processing for XML, VCF, and tab-delimited formats
Automate variant call set (VCF) annotation with clinical metadata

Use Cases

Annotating VCF files with pathogenicity data for clinical research pipelines
Identifying high-confidence pathogenic variants in specific genes like BRCA1 or CFTR
Building and updating local ClinVar databases via FTP automation