hvantk:resource-clinvar

Build Hail Table artifacts from ClinVar VCF releases for variant annotation.

Updated Feb 2, 2024

Search Tags:#bioinformatics #genomics #vcf #clinvar #variant annotation #hail

Ready to run

npx skills add https://github.com/bigbio/hvantk --skill hvantk-resource-clinvar

💬 Prompt for ChatGPT / Claude Chat▼

Please help me install this Agent Skill.
Skill: hvantk:resource-clinvar
Source: https://github.com/bigbio/hvantk/tree/main/hvantk/skills/clinvar
Command: npx skills add https://github.com/bigbio/hvantk --skill hvantk-resource-clinvar

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill requires hail, requests, click, and includes scripts (resource) components.

What problem does it solve?

This skill automates the complex process of building, updating, and managing ClinVar variant annotation tables, ensuring your genomic analysis pipeline uses the most current and accurately parsed clinical data.

Core Features & Use Cases

Automated Build Pipeline: Streamlines the transformation of raw ClinVar VCF files into optimized, queryable Hail Tables.
Lifecycle Management: Provides built-in tools for downloading, verifying, and re-processing monthly ClinVar releases.
Training Label Generation: Enables the derivation of pathogenicity training labels for machine learning models directly from ClinVar annotations.

Quick Start

Use the hvantk reprocess clinvar:variants command to build the latest ClinVar annotation table from the raw data directory.

Frequently Asked Questions about hvantk:resource-clinvar

High-intent search queries and answers about installing and using this skill.

FAQPage Schema

How do I build a Hail Table from ClinVar VCF for variant annotation?▼

To build a Hail Table from ClinVar VCF, use the automated build pipeline to parse raw VCF files into optimized, queryable Hail Tables. This streamlines transformation and ensures accurate variant annotation for genomic analysis workflows.

Can I generate pathogenicity training labels for machine learning from ClinVar annotations?▼

Yes, you can derive pathogenicity training labels for machine learning models directly from ClinVar annotations. The skill integrates clinical significance and pathogenicity classifications to facilitate training label generation.

How do I keep my ClinVar variant annotation table updated with monthly releases?▼

To keep ClinVar variant annotation tables updated, use the lifecycle management tools to download, verify, and re-process monthly ClinVar releases. This ensures your genomic pipeline uses the most current clinical data.

Does this ClinVar annotation pipeline require Hail to run?▼

Yes, Hail is a required dependency to build and manage these high-performance ClinVar variant annotation tables. The pipeline transforms raw VCF data into optimized Hail Table artifacts for multiomics analysis.

What is the best way to parse clinical significance and disease associations from ClinVar VCF files?▼

The best way to parse clinical significance and disease associations from ClinVar VCF files is using an automated build pipeline with robust parsing, validation, and provenance tracking to ensure data integrity across large-scale genomic workflows.