gevir

Integrate GeVIR and VIRLoF ranks into Hail-based variant annotation pipelines.

Updated Feb 2, 2024

Search Tags:#bioinformatics #genomics #gnomad #variant annotation #hail #gene intolerance

Ready to run

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

💬 Prompt for ChatGPT / Claude Chat▼

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

SYSTEM DOCUMENTATION & REQUIREMENTS

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

What problem does it solve?

This Skill addresses the challenge of identifying which human genes are most intolerant to functional variation, providing a standardized metric for genomic analysis and variant interpretation.

Core Features & Use Cases

Gene Intolerance Ranking: Accesses GeVIR and VIRLoF percentile ranks for over 19,000 protein-coding genes.
Multiomics Integration: Facilitates the integration of gene-level constraint metrics with variant-level data using the Hail framework.
Use Case: Researchers can use this tool to prioritize candidate genes in rare disease studies by filtering for genes with high intolerance to variation, as indicated by low GeVIR percentile ranks.

Quick Start

Use the gevir skill to process the raw metrics file and generate a Hail Table for your genomic analysis.

Frequently Asked Questions about gevir

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

FAQPage Schema

How do I quantify gene intolerance to functional variation in a genomic analysis pipeline?▼

To quantify gene intolerance to functional variation, you can use this Skill to access GeVIR and VIRLoF percentile ranks for over 19,000 protein-coding genes and structure the metrics into a Hail Table for downstream analysis.

Can I integrate gene-level constraint metrics with variant-level data using Hail?▼

Yes, you can integrate gene-level constraint metrics with variant-level data using Hail by processing the raw intolerance metrics file to generate a structured Hail Table for your genomic research workflows.

What are GeVIR and VIRLoF percentile ranks used for in rare disease studies?▼

GeVIR and VIRLoF percentile ranks are used to prioritize candidate genes in rare disease studies by filtering for genes with high intolerance to variation, indicated by low percentile ranks.

Do I need the Hail library to process gene intolerance metrics for variant annotation?▼

Yes, you need the Hail library installed as a required dependency to process the raw metrics file and structure the gene-level data for integration into variant annotation pipelines.

How many protein-coding genes are covered by gene intolerance ranking metrics?▼

Gene intolerance ranking metrics provide GeVIR and VIRLoF percentile ranks for over 19,000 protein-coding genes to quantify vulnerability to functional variation.