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ensembl-gene

Parse Ensembl GTF files into a per-gene Hail Table with structural and coordinate metadata.

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

SYSTEM DOCUMENTATION & REQUIREMENTS

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

What problem does it solve?

This Skill provides a reliable, version-controlled source of truth for gene-level annotations, preventing inconsistencies in multiomics pipelines caused by varying gene model definitions.

Core Features & Use Cases

  • Canonical Gene Mapping: Provides a unified table of gene IDs, names, biotypes, and coordinates derived from pinned Ensembl GTF releases.
  • Structural Covariates: Calculates essential metrics like CDS length, coding-exon counts, and MANE Select transcript assignments for downstream normalization.
  • Use Case: Researchers can use this to normalize PTM site density or adjust for gene length as a nuisance covariate in rare-variant burden analysis.

Quick Start

Use the ensembl-gene skill to download and build the canonical gene structure table for the currently pinned Ensembl release.

Frequently Asked Questions about ensembl-gene

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

FAQPage Schema
How do I parse Ensembl GTF files into a Hail Table for gene-level annotation?▼

You can parse Ensembl GTF files into a standardized Hail Table containing structural and coordinate metadata to support multiomics integration workflows. This provides consistent gene-level covariates for downstream variant annotation and burden analysis.

What is the best way to standardize gene models for multiomics integration?▼

Standardizing gene models for multiomics integration involves parsing pinned Ensembl GTF releases into a per-gene table with deterministic build provenance. This prevents pipeline inconsistencies caused by varying gene model definitions across different releases.

How do I calculate structural covariates like CDS length from Ensembl gene annotations?▼

Structural covariates like CDS length, coding-exon counts, and MANE Select transcript assignments are calculated by parsing the structural metadata in Ensembl GTF files. These metrics are essential for normalizing PTM site density or adjusting for gene length in burden analysis.

Does this gene annotation approach support deterministic build provenance and versioning?▼

Yes, this approach supports deterministic build provenance, stable gene model versioning, and drift detection via HTTP headers. These features ensure you are using a reliable, version-controlled source of truth for canonical gene mapping.

Can I use pandas and Hail to build a canonical gene mapping from Ensembl releases?▼

Yes, using Hail and pandas you can build a unified table of gene IDs, names, biotypes, and coordinates derived from pinned Ensembl GTF releases. This provides a consistent source of truth for multiomics pipelines requiring gene-level annotations.

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