genomic-coordinates
genomic-coordinates is a Bioinformatics & life sciences skill for AI agents, published by K-Dense-AI in the scientific-agent-skills repository on GitHub. Skillspace rates genomic-coordinates C (74/100) and it passed the safety scan; a judge model has also reviewed it.
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".
- Grade
- C
- Quality
- 74 / 100
- Safety
- Passed
- GitHub stars
- 44,723
Placed #1 of 6 in the judged category final for Bioinformatics & life sciences.
This rating describes the version of the repository we crawled; it may have changed since, so go by its current files.
Our review
- Architecture
- 100 / 100
- Maturity
- Basic: a single SKILL.md
- Security scan
- No issues found
- License
- Not declared. Check the repository before reusing it.
Judge review
Placed #1 of 6 in the judged category final for Bioinformatics & life sciences.
- Trigger
93 93 - Instructions
95 95 - Specificity
97 97 - Safety
95 95 - Disclosure
92 92 - Maintenance
88 88
Teaches the coordinate-and-variant mental model with runnable converters, real sample outputs, and sharp edge cases like GRCh37/hg19's 2-byte mitochondrial difference, making it the most rigorous and concrete skill in the set.
Not checked yet
- Category is a classifier prediction; no model has read this skill yet
- No blind task eval yet
- Scope (portable / vendor / repo-internal) not assessed; only the top of each category is read for scope
- Sibling files (scripts, references) not fetched; security scan covers SKILL.md only
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