Parse Ensembl GTF files into per-gene structural summary tables.
npx skills add https://github.com/bigbio/hvantk --skill ensembl-gene-structure
Please help me install this Agent Skill. Skill: ensembl-gene:structure Source: https://github.com/bigbio/hvantk/tree/main/hvantk/skills/ensembl_gene/structure Command: npx skills add https://github.com/bigbio/hvantk --skill ensembl-gene-structure
This skill resolves the ambiguity and inconsistency in gene structural data by providing a standardized, pinned table of Ensembl gene coordinates, biotypes, and coding metrics derived from a specific GTF release.
Run the hvantk reprocess ensembl-gene:structure command to build the canonical gene table from the pinned Ensembl GTF release.
High-intent search queries and answers about installing and using this skill.
To parse Ensembl GTF files into a standardized structural summary, this Skill extracts per-gene coordinates, biotypes, and coding transcript metrics. It processes the pinned GTF release using pandas to generate a consistent table for downstream pipelines.
Selecting the MANE Select transcript for variant annotation requires deterministic transcript selection from gene models. This Skill automatically identifies the MANE Select transcript or falls back to the longest coding transcript to serve as the representative model.
Calculating gene-length-adjusted rare-variant burden counts in Hail requires stable gene structural metrics. This Skill generates a standardized table of CDS lengths and coordinates, satisfying requirements for nuisance covariate calculation in multiomics integration.
This Ensembl gene structure parser requires hail, pandas, requests, and click to run. These dependencies support the parsing logic and enable the generation of standardized per-gene structural summary tables from a pinned GTF release.
You need a standardized Ensembl gene structure table for multiomics integration to resolve ambiguity and inconsistency in gene structural data. It provides consistent gene location, name, biotype, and CDS length across all downstream analyses.
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