genomic-coordinates

Editorial and source context

What this Skill does

Genomic Coordinates is a source-indexed Agent Skill for design & frontend work. Based on the SKILL.md description, it focuses on convert genomic intervals between coordinate conventions, normalise and compare variant…. Use the linked GitHub file to confirm scope and prerequisites before enabling it.

What the author says

Convert genomic intervals between coordinate conventions, normalise and compare variant representations, and detect assembly or contig-naming mismatches before they corrupt an analysis. Use whenever coordinates cross a format, tool, or assembly boundary - converting between BED, GFF/GTF, VCF, SAM/BAM, WIG, PSL, genePred, Picard interval_list, or region strings; reconciling 0-based half-open with 1-based inclusive; left-aligning or trimming indels; checking whether two variant records describe the same change; mapping genomic to transcript, CDS, or protein positions; auditing a BED/GTF/VCF for convention violations; or diagnosing GRCh37 vs hg19 vs GRCh38 vs T2T, chr-prefix, and liftover problems. Triggers include "off by one", "0-based", "1-based", "half-open", "coordinate system", "left-align", "normalize variant", "bcftools norm", "chr prefix", "wrong genome build", "liftover", "REF mismatch", and "HGVS".

Compatibility and requirements

• Use an agent runtime that supports Agent Skills and the linked SKILL.md format.
• Confirm the source repository's tools, SDKs, and platform prerequisites for ui and frontend work.

How to install or import it

• Open the linked GitHub SKILL.md and review its scope and setup instructions.
• Install or import the skill using the agent runtime's documented workflow.
• Run a small, non-sensitive test and verify the output before broader use.

Permissions and risks

• Review every command, file path, network request, dependency, and credential scope before enabling it.
• GitHub stars indicate popularity, not safety or correctness; validate the source and test with non-sensitive data.

Example workflows

• Ask an AI agent to apply Genomic Coordinates to ui and frontend work described in the source record.
• Have the agent state assumptions, required tools, and expected output before using this design & frontend skill.
• Compare the result with the linked GitHub SKILL.md and verify it against your project requirements.