Can I use this for clinical diagnosis?

No, ClinVar data is for research purposes. All clinical findings should be interpreted and verified by a qualified genetics professional.

Does it support bulk data formats like XML and VCF?

Yes, it includes technical patterns for parsing large-scale XML variation archives and using bcftools to annotate VCF files.

How does this skill access ClinVar data?

It utilizes NCBI's E-utilities API for live queries and provides documented methods for downloading and processing bulk datasets from the official ClinVar FTP site.

How does it handle conflicting variant classifications?

It provides a resolution strategy that prioritizes high-confidence star ratings, expert panel reviews, and the most recent submission dates.

Does it support both GRCh37 and GRCh38 genome builds?

Yes, the skill provides specific instructions for downloading and annotating VCF files corresponding to both GRCh37 and GRCh38 coordinates.

ClinVar Database Integration

Name: ClinVar Database Integration
Author: Yezez9

byYezez9

0•

データサイエンスとML

Queries NCBI ClinVar for genetic variant clinical significance and provides tools for pathogenicity interpretation and genomic data annotation.

The ClinVar Database skill enables bioinformaticians and researchers to interact seamlessly with NCBI's archive of human genetic variants and their relationship to health phenotypes. It facilitates searching for variants by gene or condition, interpreting ACMG/AMP pathogenicity classifications, and accessing data through E-utilities APIs or bulk FTP downloads. Whether you are annotating VCF files for clinical pipelines or analyzing conflicting variant interpretations, this skill provides the domain-specific guidance and implementation patterns needed to integrate ClinVar data into genomic research and medicine workflows.

主な機能

01Programmatic access via NCBI E-utilities API and curl

020 GitHub stars

03Standardized interpretation of ACMG/AMP pathogenicity classifications

04Bulk data processing for XML, VCF, and tab-delimited formats

05Conflict resolution strategies for variant interpretations

06Automated VCF annotation using bcftools and Python integration

ユースケース

01Building local bioinformatics databases from monthly ClinVar FTP releases

02Identifying high-confidence pathogenic variants for specific genes in clinical research

03Annotating variant call sets (VCFs) with clinical significance for genomic pipelines

What are Skills?·How to Install

Install with 🐟 Skill.Fish

npx skillfish add yezez9/research-agent clinvar-database

For use in Claude.ai and ChatGPT

主な機能

01Programmatic access via NCBI E-utilities API and curl

020 GitHub stars

03Standardized interpretation of ACMG/AMP pathogenicity classifications

04Bulk data processing for XML, VCF, and tab-delimited formats

05Conflict resolution strategies for variant interpretations

06Automated VCF annotation using bcftools and Python integration

ユースケース

01Building local bioinformatics databases from monthly ClinVar FTP releases

02Identifying high-confidence pathogenic variants for specific genes in clinical research

03Annotating variant call sets (VCFs) with clinical significance for genomic pipelines