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hvantk:resource-clingen

Convert ClinGen Gene-Disease Validity CSV data into Hail Tables.

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

SYSTEM DOCUMENTATION & REQUIREMENTS

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

What problem does it solve?

This Skill automates the complex process of downloading, cleaning, and transforming raw ClinGen Gene-Disease Validity CSV data into high-performance Hail Tables, ensuring your genomic analysis pipelines always use the most current, validated associations.

Core Features & Use Cases

  • Automated Pipeline: Handles the entire lifecycle from real-time data acquisition to schema-validated Hail Table generation.
  • Data Integrity: Implements robust drift detection and schema validation to prevent silent failures in downstream genomic joins.
  • Use Case: Researchers can use this to instantly refresh their variant annotation databases with the latest ClinGen expert-curated gene-disease classifications without manual CSV parsing or re-formatting.

Quick Start

Use the hvantk clingen-download skill to fetch the latest gene-disease validity dataset and then run the reprocess command to build the updated Hail Table.

Frequently Asked Questions about hvantk:resource-clingen

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

FAQPage Schema
How do I convert ClinGen gene-disease validity data into Hail Tables for variant annotation?▼

Converting ClinGen gene-disease validity data into Hail Tables is automated by ingesting raw CSV files, applying schema-aware parsing, and outputting structured tables for high-performance genomic variant annotation joins.

Why does my genomic annotation pipeline fail silently when ClinGen CSV columns change?▼

Genomic annotation pipelines fail silently during ClinGen CSV column changes because of schema drift; implementing automated drift detection and schema validation prevents these silent failures in downstream data joins.

What's the best way to automate continuous integration for ClinGen expert-curated data downloads?▼

Automating continuous integration for ClinGen data downloads involves orchestrating real-time data acquisition, schema-aware parsing, and drift detection to maintain updated expert-curated gene-disease validity classifications.

Do I need Hail installed to process ClinGen gene-disease validity CSV files?▼

Hail is required to process ClinGen gene-disease validity CSV files into structured Hail Tables, alongside standard Python scientific libraries like pandas and requests to execute ingestion and transformation.

Can I use pandas to parse ClinGen data for genomic variant association lookups?▼

Pandas can parse ClinGen data initially, but transforming it into structured Hail Tables is necessary to enable high-performance genomic variant annotation and expert-curated association lookups at scale.

hvantk:resource-clingen: What are the limitations of using automated pipelines for ClinGen data ingestion?▼

Automated pipelines for ClinGen data ingestion are limited by their dependency on Hail and Python scientific libraries, requiring continuous drift detection and schema validation to prevent downstream genomic join failures.

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