Individual skill

genomic-coordinates

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".

backend/cli/skills/biology/genomic-coordinates/SKILL.md

Source commit a08e0ad0ad3d6448123039ee4659163eb2e35d99

What was checked

Matches the observed repository HEAD

Yes

Scanner rules are current

Yes

Repository scan complete

No

Skill scan complete

No

Observed behavior

Network or broad shell

Last checked

Nov 2, 2026

These are observations at the recorded commit, not a guarantee of safety. Review the source before running it.

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