genomic-coordinates

SUMMARY

What it does

This skill provides scripts and guidance for converting genomic coordinates between formats and assemblies, normalizing and comparing variant representations, and auditing files for coordinate convention violations. It includes command-line tools for coordinate conversion, variant normalization, contig/assembly checking, and interval auditing. The skill is designed for use in bioinformatics workflows where coordinate errors can silently corrupt analyses. It requires Python 3.11+ and uses only the standard library; variant normalization requires a reference FASTA. The skill is distributed under the MIT license.