What clinical significance classifications are supported?

It covers standardized ACMG/AMP terms including Pathogenic, Likely Pathogenic, Uncertain Significance (VUS), Likely Benign, and Benign, along with star-rating confidence levels.

How does the skill handle conflicting variant interpretations?

It provides a multi-step resolution strategy that prioritizes higher star ratings (expert panel reviews), newer submission dates, and population frequency data.

How do I access ClinVar data programmatically using this skill?

The skill provides detailed implementation patterns for using NCBI's E-utilities API (esearch, efetch) and scripts for accessing the public FTP site for bulk XML and VCF downloads.

Can I use this skill to annotate my own VCF files?

Yes, the skill includes specific command-line and Python examples for using tools like bcftools and PyVCF to annotate variant calls with ClinVar clinical significance metadata.

ClinVar Database Helper

Name: ClinVar Database Helper
Author: youyinnn

byyouyinnn

0•

データサイエンスとML

Integrates NCBI ClinVar data to interpret genetic variants, query clinical significance, and process genomic datasets.

This skill empowers developers and bioinformaticians to seamlessly interact with the NCBI ClinVar database, providing comprehensive guidance for querying variant pathogenicity, downloading bulk datasets via FTP, and programmatically accessing the E-utilities API. It simplifies the interpretation of clinical significance classifications based on ACMG/AMP guidelines, provides strategies for resolving conflicting variant data using star-rating confidence systems, and offers production-ready code patterns for annotating VCF files and processing large XML archives in genomic medicine pipelines.

主な機能

01Bulk data processing workflows for VCF, XML, and tab-delimited formats

020 GitHub stars

03Automated VCF annotation workflows using bcftools and Python

04Interpretation guidelines for ACMG/AMP clinical significance classifications

05Advanced filtering for pathogenic variants and high-confidence star ratings

06Programmatic access via NCBI E-utilities API (esearch, esummary, efetch)

ユースケース

01Annotating genomic variant call sets (VCF) with clinical significance data for diagnostics

02Conducting gene-specific research to identify variants associated with hereditary conditions

03Building automated pipelines to monitor updates in variant classifications over time

What are Skills?·How to Install

Install with 🐟 Skill.Fish

npx skillfish add youyinnn/skills-collection clinvar-database

For use in Claude.ai and ChatGPT

主な機能

01Bulk data processing workflows for VCF, XML, and tab-delimited formats

020 GitHub stars

03Automated VCF annotation workflows using bcftools and Python

04Interpretation guidelines for ACMG/AMP clinical significance classifications

05Advanced filtering for pathogenic variants and high-confidence star ratings

06Programmatic access via NCBI E-utilities API (esearch, esummary, efetch)

ユースケース

01Annotating genomic variant call sets (VCF) with clinical significance data for diagnostics

02Conducting gene-specific research to identify variants associated with hereditary conditions

03Building automated pipelines to monitor updates in variant classifications over time