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hvantk:resource-gwas-catalog

Build a structured Hail Table from EBI GWAS Catalog TSV files.

Updated Feb 2, 2024
Search Tags:#data engineering#bioinformatics#genomics#gwas#variant annotation#hail
One-click install
npx skills add https://github.com/bigbio/hvantk --skill hvantk-resource-gwas-catalog
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: hvantk:resource-gwas-catalog
Source: https://github.com/bigbio/hvantk/tree/main/hvantk/skills/gwas_catalog
Command: npx skills add https://github.com/bigbio/hvantk --skill hvantk-resource-gwas-catalog

SYSTEM DOCUMENTATION & REQUIREMENTS

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

What problem does it solve?

This skill solves the challenge of integrating large-scale, heterogeneous GWAS Catalog association data into Hail-based multiomics pipelines by providing a standardized, reproducible build process.

Core Features & Use Cases

  • Automated ETL: Transforms raw EBI GWAS Catalog TSV files into structured, keyed Hail Tables.
  • Variant Normalization: Implements consistent keying by (locus, alleles) with sentinel ALT values to facilitate seamless joins with other variant datasets like ClinVar or gnomAD.
  • Use Case: Researchers can use this skill to quickly ingest the latest GWAS Catalog release to annotate their variant tables with trait associations, p-values, and effect sizes for downstream burden or enrichment analysis.

Quick Start

Use the hvantk reprocess command to build the gwas-catalog associations dataset from your local raw TSV file.

Frequently Asked Questions about hvantk:resource-gwas-catalog

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

FAQPage Schema
How do I load EBI GWAS Catalog data into a Hail Table for variant annotation?▼

You can build a Hail Table from the EBI GWAS Catalog TSV by running the hvantk reprocess command, which automates the ETL process and outputs a keyed table for genomic joins.

Does this GWAS Catalog ingestion skill require a distributed computing environment?▼

Yes, building the GWAS Catalog Hail Table requires Hail for distributed computation to process large-scale association data and execute the underlying variant normalization logic.

How are variants normalized when building Hail Tables from GWAS Catalog data?▼

Variants are normalized by implementing consistent keying by locus and alleles, using sentinel ALT values to facilitate seamless joins with other variant datasets like ClinVar or gnomAD.

Can I use Hail to join GWAS Catalog trait associations with existing variant datasets?▼

Yes, you can use Hail to join GWAS Catalog trait associations with existing variant datasets, enabling you to annotate your variant tables with p-values and effect sizes for downstream analysis.

What filtering logic is applied when processing the EBI GWAS Catalog TSV?▼

The processing applies specific filtering logic for canonical chromosome contigs and risk allele identification to ensure the resulting Hail Table contains standardized GWAS associations.

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