gnomad-metrics

Download gnomAD constraint tables and build Hail Tables with schema validation.

Updated Feb 2, 2024

Search Tags:#bioinformatics #genomics #gnomad #variant annotation #hail #constraint metrics

Ready to run

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

💬 Prompt for ChatGPT / Claude Chat▼

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

SYSTEM DOCUMENTATION & REQUIREMENTS

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

What problem does it solve?

This Skill addresses the difficulty of manually acquiring and integrating standardized gnomAD constraint metrics into variant analysis pipelines, ensuring consistent gene-level intolerance scoring.

Core Features & Use Cases

Automated Data Acquisition: Downloads specific gnomAD constraint tables (v2.1.1 or v4.0) directly from public GCS buckets.
Hail Table Construction: Reprocesses raw TSV/BGZ files into optimized Hail Tables with proper provenance and schema validation.
Use Case: Researchers can use this to quickly annotate a cohort of variants with pLI and oe_lof scores to prioritize genes for pathogenicity analysis.

Quick Start

Use the gnomad-metrics skill to download the default v2.1.1 constraint table and build it into a Hail Table for your analysis.

Frequently Asked Questions about gnomad-metrics

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

FAQPage Schema

How do I integrate gnomAD constraint metrics into a Hail Table?▼

This Skill automates downloading raw gnomAD constraint TSV or BGZ files from public GCS buckets and reprocesses them into optimized Hail Tables with proper schema validation for genomics research.

What are gnomAD gene constraint metrics used for in variant annotation?▼

gnomAD gene constraint metrics, such as pLI and oe_lof scores, are used in variant annotation workflows to measure gene-level intolerance and prioritize genes for pathogenicity analysis. This Skill acquires v2.1.1 or v4.0 data for this purpose.

Can I use Hail to annotate variants with pLI and oe_lof scores from gnomAD v4.0?▼

Yes, this Skill supports multi-version constraint data integration, allowing you to download and build the gnomAD v4.0 constraint table directly into your Hail environment for variant annotation.

Does this gnomAD metrics Skill support automated drift detection and reproducible builds?▼

Yes, this Skill supports automated drift detection and reproducible data builds. It ensures consistent gene-level intolerance scoring by applying schema provenance and validation during the Hail Table construction process.

What is the best way to acquire standardized gnomAD constraint tables for genomics pipelines?▼

The best way to acquire standardized gnomAD constraint tables is automating the download process from public GCS buckets. This ensures consistent gene-level intolerance scoring and schema provenance for your variant analysis pipelines.