What is the primary use of the ClinVar Database skill?

It is used to query and interpret the relationship between human genetic variants and health conditions using NCBI data archive resources.

Does this skill support both GRCh37 and GRCh38 builds?

Yes, the skill provides instructions for accessing and processing ClinVar datasets for both the GRCh37 and GRCh38 human genome assemblies.

Can I use this skill to annotate VCF files?

Yes, it provides specific commands and code patterns for using tools like bcftools to annotate VCF files with ClinVar metadata such as clinical significance.

How does the skill handle rate limits for NCBI E-utilities?

The skill provides guidance on using API keys to increase request limits and implementing exponential backoff for stable programmatic access.

What do the star ratings in ClinVar signify?

Star ratings represent the review status and level of confidence in a variant's classification, ranging from single submitters (1 star) to expert panel reviews (3-4 stars).

ClinVar Genetic Variant Database

Name: ClinVar Genetic Variant Database
Author: Activer007

byActiver007

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Data Science & ML

Accesses and interprets NCBI ClinVar data to evaluate the clinical significance and pathogenicity of human genetic variants.

The ClinVar Database skill provides comprehensive tools for interacting with the NCBI ClinVar archive, allowing developers and researchers to query variant pathogenicity, clinical significance, and supporting evidence. It facilitates seamless access via the E-utilities API and FTP bulk downloads, supports VCF file annotation for genomic pipelines, and offers expert guidance on interpreting ACMG/AMP classifications. Whether you are building bioinformatics pipelines or performing targeted genetic research, this skill streamlines the process of resolving conflicting interpretations and accessing high-confidence genomic data.

Key Features

01Support for bulk data processing from monthly and weekly FTP releases

02Interpret ACMG/AMP pathogenicity classifications and star-rated review statuses

030 GitHub stars

04Query variants by gene, condition, or clinical significance using NCBI's E-utilities API

05Automate VCF annotation with clinical significance, review status, and disease names

06Resolve conflicting variant interpretations through evidentiary review strategies

Use Cases

01Building local bioinformatics pipelines with periodic ClinVar data synchronization

02Searching for high-confidence pathogenic variants associated with specific hereditary conditions

03Annotating genomic call sets for clinical interpretation and research report generation

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

Download Skill