genomic-coordinates SKILL.md skillA
genomic-coordinates from k-dense-ai/scientific-agent-skills is an agent skill: a SKILL.md folder an AI agent loads when a task calls for it.
mdr add k-dense-ai/scientific-agent-skills/genomic-coordinates@v1.3Pins v1.3 in mdr.lock. Pin the fingerprint instead.
- Audit grade
- A, 17 of 17 checks passed
- Kind
- SKILL.md skill
- Repository
- k-dense-ai/scientific-agent-skills
- Path
skills/genomic-coordinates/SKILL.md- Versions recorded
- 4
- Latest version
- v1.3, committed Oct 1, 2026
- First version recorded
- Jul 26, 2026
- Size
- 12,764 bytes
- Repository stars
- 56,497
- License
- MIT
Converts genomic intervals between coordinate conventions, normalises and compares variant representations, and detects assembly or contig-naming mismatches before they corrupt an analysis. Used 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…
Collected from public GitHub. Every version is saved exactly as it was and never changes. Install it at an exact version with the mdr tool, and every file is checked before it reaches your agent. The main file is checked against the SHA-256 fingerprint recorded here, and the others against the fingerprints GitHub keeps for its source commit. The automatic checks below grade the latest version, and the same checks always give the same file the same grade.
What the file says
# Genomic Coordinates ## When to use Any time a coordinate crosses a boundary: between two file formats, between two tools, between two assemblies, or between the genome and a transcript. ## The rule **A coordinate is three facts, not one: the number, the convention it is written in, and the assembly it was measured against.** Carry all three or the number is not interpretable. Coordinate errors are the quietest class of bug in genomics. An off-by-one BED file parses, sorts, and intersects without complaint. A GRCh37 VCF joined against a GRCh38 annotation returns rows. A right-shifted indel simply fails to match its entry in ClinVar, and the result is a variant reported as novel. Nothing raises an error; the answer is just wrong, and it is wrong in a direction that looks plausible. So: convert with the table, not from memory, and verify against the reference whenever a reference is available. ## The two conversions ``` 1-based inclusive -> 0-based half-open : start - 1, end 0-based half-open -> 1-based inclusive : start + 1, end ``` These formulas apply to nonempty spans on the same reference and strand. They do …
Read the whole file at its exact version.
How to install
mdr add k-dense-ai/scientific-agent-skills/genomic-coordinates@sha256:da3eee43dfee06eeThe line at the top of this page pins the label v1.3, which is what most people want. This one pins the sha256 fingerprint of the contents instead, so it survives a label being moved. Either way the exact version is written to mdr.lock, and mdr install downloads and checks those contents again, so it installs them exactly or stops with an error.
[](https://markdownregistry.com/a/art_qckvkqncemqpnwp7)
3 badge image fetches in 30 days. What the badge shows.
Versions
The registry has recorded 4 versions of this file, between Jul 26, 2026 and Oct 1, 2026, about one every 22 days.
| version | committed | commit | size | audit | |
|---|---|---|---|---|---|
| v1.3 latest | 2026-10-01 | a92663a | 12,764 B | A | view · diff |
| v1.2 | 2026-09-30 | ce9e6e9 | 10,287 B | A | view · diff |
| v1.1 | 2026-09-02 | 1e5eeff | 10,040 B | A | view · diff |
| v1.0 | 2026-07-26 | ce67928 | 9,082 B | A | view |
Audit of the latest version
- pass: Frontmatter block present
- pass: Frontmatter declares a name
- pass: Frontmatter declares a description
- pass: Size between 200 bytes and 200 KB (12764 bytes)
- pass: No zero-width or bidi control characters
- pass: No instruction hidden inside an HTML comment
- pass: No link to an exfiltration or paste host
- pass: No credential-shaped string
- pass: No instruction to send local credentials anywhere
- pass: No text hidden with inline styles
- pass: No prompt-injection phrasing
- pass: No curl or wget piped into a shell
- pass: No recursive delete of root, home or parent
- pass: No instruction to read or print local credentials
- pass: No base64 blob over 200 characters
- pass: No link to a raw IP address
- pass: No script tag
Source
k-dense-ai/scientific-agent-skills · 56,497 stars · license MIT · pushed 2026-11-02 · branch main
API
GET https://markdownregistry.com/api/v1/artifacts/art_qckvkqncemqpnwp7 GET https://markdownregistry.com/api/v1/resolve?ref=k-dense-ai/scientific-agent-skills/genomic-coordinates GET https://markdownregistry.com/api/v1/blob/da3eee43dfee06ee632388ddda0c38bb0bc57ec33420cbf26b14ce86be3c28a0
Your AI assistant does the legwork. You hear about the deals worth your word. Hand yours the standing instructions at modelranch.com and it joins the network that reads files like this one.
Guides: the SKILL.md format and its required fields · what to check before you install a skill · how to pin a skill to an exact version · where to find agent skills · keeping a team on the same skills · which agent file does what.