How do I search for pathogenic variants in a specific gene?

You can use specific search patterns such as 'BRCA1[gene] AND pathogenic[CLNSIG]' via the web interface or programmatically through the E-utilities API.

What is ClinVar used for in bioinformatics?

ClinVar is a public archive that aggregates reports on the relationships between human genetic variants and phenotypes, providing standardized classifications like pathogenic, benign, or VUS.

Can I use this skill to process large VCF files?

Yes, the skill provides patterns for using tools like bcftools and Python to annotate, filter, and analyze ClinVar VCF data for both GRCh37 and GRCh38 builds.

How should I handle conflicting variant interpretations?

The skill suggests prioritizing higher star ratings, checking submission dates for recent evidence, and reviewing population frequency data like gnomAD to resolve conflicts.

What do the ClinVar star ratings indicate?

Star ratings represent the review status: 4 stars for practice guidelines, 3 for expert panels, 2 for multiple submitters without conflict, 1 for single submitters, and 0 for no criteria provided.

ClinVar Database Integration

Name: ClinVar Database Integration
Author: Activer007

byActiver007

0•

数据科学与机器学习

Accesses and interprets NCBI ClinVar data to evaluate human genetic variants, clinical significance, and phenotype relationships.

This skill empowers Claude to interact with the NCBI ClinVar archive, providing comprehensive support for genomic medicine and bioinformatics workflows. It enables users to search for variants by gene or condition, interpret ACMG/AMP clinical significance classifications, and programmatically access data via E-utilities API or bulk FTP downloads. Whether you are annotating VCF files, resolving conflicting variant interpretations, or building local genomic databases, this skill provides the patterns and best practices needed to handle complex genetic evidence and standardized pathogenicity reporting.

主要功能

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

02Programmatic access via NCBI E-utilities API including esearch and efetch

030 GitHub stars

04Expert interpretation of pathogenicity classifications and ACMG/AMP guidelines

05Standardized variant search by gene, chromosome, or clinical significance

06Conflict resolution strategies for multiple variant interpretation submissions

使用场景

01Identifying pathogenic variants for specific genes or hereditary conditions

02Building local bioinformatic pipelines for variant interpretation and reporting

03Annotating variant call sets (VCFs) with high-confidence clinical data

What are Skills?·How to Install

Install with 🐟 Skill.Fish

npx skillfish add activer007/ordinary-claude-skills clinvar-database

For use in Claude.ai and ChatGPT

主要功能

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

02Programmatic access via NCBI E-utilities API including esearch and efetch

030 GitHub stars

04Expert interpretation of pathogenicity classifications and ACMG/AMP guidelines

05Standardized variant search by gene, chromosome, or clinical significance

06Conflict resolution strategies for multiple variant interpretation submissions

使用场景

01Identifying pathogenic variants for specific genes or hereditary conditions

02Building local bioinformatic pipelines for variant interpretation and reporting

03Annotating variant call sets (VCFs) with high-confidence clinical data

What are Skills?·How to Install

Install with 🐟 Skill.Fish

npx skillfish add activer007/ordinary-claude-skills clinvar-database

For use in Claude.ai and ChatGPT