How do I handle API rate limits?

The skill provides best practices such as using NCBI API keys to increase limits and implementing exponential backoff for programmatic requests.

What are the ClinVar star ratings?

They represent the review status of a variant classification, ranging from 0 stars (no criteria) to 4 stars (practice guideline), indicating level of confidence.

Does it support the latest genome builds?

Yes, it provides guidance and download paths for both GRCh37 and GRCh38 genome assemblies.

How does this skill help with VCF files?

It provides specific commands and scripts using bcftools and Python to annotate your VCF files with ClinVar clinical significance data.

Can I use this for bulk data analysis?

Yes, the skill includes patterns for downloading and parsing multi-GB XML and tab-delimited files from the ClinVar FTP site.

ClinVar Database Explorer

Name: ClinVar Database Explorer
Author: Microck

byMicrock

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Data Science & ML

Queries and interprets genomic variant data from the NCBI ClinVar database to support clinical genetics and research workflows.

About

The ClinVar Database skill enables developers and researchers to interact seamlessly with NCBI's archive of human genetic variants and their relationships to health. It provides comprehensive guidance for querying variants by gene or condition, interpreting pathogenicity classifications using ACMG/AMP standards, and automating data retrieval via the E-utilities API. Whether you are annotating VCF files for a bioinformatics pipeline or resolving conflicting variant interpretations, this skill streamlines the process of integrating clinical genomic data into your applications.

Key Features

Programmatic access using NCBI E-utilities API with rate-limit handling
Integration workflows for VCF annotation using tools like bcftools
Advanced variant searching by gene, condition, and clinical significance
Automated bulk data retrieval from ClinVar FTP servers in XML and VCF formats
Standardized interpretation of pathogenicity classifications and star ratings
81 GitHub stars

Use Cases

Annotating patient VCF files with clinical significance for genomic medicine pipelines
Automating the monitoring of updated variant classifications for clinical decision support
Conducting bulk analysis of disease-specific genetic variants for research projects

About

Key Features

Programmatic access using NCBI E-utilities API with rate-limit handling
Integration workflows for VCF annotation using tools like bcftools
Advanced variant searching by gene, condition, and clinical significance
Automated bulk data retrieval from ClinVar FTP servers in XML and VCF formats
Standardized interpretation of pathogenicity classifications and star ratings
81 GitHub stars

Use Cases

Annotating patient VCF files with clinical significance for genomic medicine pipelines
Automating the monitoring of updated variant classifications for clinical decision support
Conducting bulk analysis of disease-specific genetic variants for research projects