Can I use this skill to automate VCF file annotation?

Yes, the skill provides specific implementation patterns using bcftools and Python to annotate your variant call sets with clinical significance and review status.

How does the skill handle conflicting variant interpretations?

It provides a structured resolution strategy that prioritizes star ratings (review status), expert panel classifications, and submission dates to determine the most reliable classification.

Are the data formats like XML and VCF covered?

Yes, the skill details how to download and parse various formats from the ClinVar FTP site, including VCV XML files and genome-build-specific VCFs (GRCh37/GRCh38).

Does it support programmatic access to NCBI?

Absolutely. It includes documentation and code examples for using NCBI's E-utilities API (esearch, esummary, efetch) and best practices for managing rate limits.

What is the primary purpose of the ClinVar skill?

It serves as a specialized guide for interacting with the NCBI ClinVar database, helping users search for genetic variants, interpret clinical significance, and process large-scale genomic data.

ClinVar Genetic Variant Analysis

Name: ClinVar Genetic Variant Analysis
Author: Microck

byMicrock

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데이터 과학 및 ML

Queries and interprets NCBI ClinVar data to identify the clinical significance of human genetic variants.

소개

ClinVar Genetic Variant Analysis is a specialized Claude Code skill designed for researchers, bioinformaticians, and developers working in genomic medicine. It provides comprehensive guidance on querying NCBI's ClinVar database to identify relationships between human genetic variants and phenotypes. The skill streamlines the process of searching by gene or condition, interpreting pathogenicity classifications using ACMG/AMP standards, and accessing data programmatically via E-utilities APIs or bulk FTP downloads. It is an essential tool for those looking to annotate VCF files, resolve conflicting variant interpretations, or build localized genomic databases.

주요 기능

Expert strategies for resolving conflicting variant interpretations
Advanced search patterns for genes, conditions, and clinical significance
Automated workflows for VCF annotation and bulk XML/Tab-delimited processing
Programmatic integration with NCBI E-utilities API and Biopython
Standardized interpretation of ACMG/AMP pathogenicity classifications
89 GitHub stars

사용 사례

Annotating variant call sets (VCF) with high-confidence clinical significance data
Automating the retrieval of pathogenic variants for specific hereditary disorders
Building and maintaining local genomic databases using monthly ClinVar releases

소개

주요 기능

Expert strategies for resolving conflicting variant interpretations
Advanced search patterns for genes, conditions, and clinical significance
Automated workflows for VCF annotation and bulk XML/Tab-delimited processing
Programmatic integration with NCBI E-utilities API and Biopython
Standardized interpretation of ACMG/AMP pathogenicity classifications
89 GitHub stars

사용 사례

Annotating variant call sets (VCF) with high-confidence clinical significance data
Automating the retrieval of pathogenic variants for specific hereditary disorders
Building and maintaining local genomic databases using monthly ClinVar releases