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liftover-coordinates SKILL.md skillA

This file is byte-identical to the first copy the registry indexed. Same content hash, so the same checks give both the same grade.

liftover-coordinates from ammawla/encode-toolkit is an agent skill: a SKILL.md folder an AI agent loads when a task calls for it.

Install it, pinned

mdr add ammawla/encode-toolkit/liftover-coordinates@git:20260920.6050003

Pins git:20260920.6050003 in mdr.lock. Pin the fingerprint instead.

Audit grade: A, 17 of 17 checks passed
Kind: SKILL.md skill
Repository: ammawla/encode-toolkit
Path: plugin/skills/liftover-coordinates/SKILL.md
Versions recorded: 3
Latest version: git:20260920.6050003, committed Sep 20, 2026
First version recorded: Mar 12, 2026
Size: 23,330 bytes
Repository stars: 21
License: AGPL-3.0

Convert genomic coordinates between assembly versions (GRCh37/hg19 to GRCh38/hg38, mm9 to mm10). Guides UCSC liftOver for BED files, CrossMap for VCF/bigWig, and handles unmapped regions with provenance logging.

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

# Convert Genomic Coordinates Between Assembly Versions

## When to Use

- User needs to convert genomic coordinates between assemblies (hg19↔hg38, mm9↔mm10)
- User asks about "liftover", "coordinate conversion", "assembly mismatch", or "CrossMap"
- User has data in hg19/GRCh37 that needs conversion to GRCh38 (or vice versa) before integration
- User wants to use UCSC liftOver or CrossMap for BED, VCF, bigWig, or BAM files
- Example queries: "convert my hg19 peaks to hg38", "liftover coordinates for integration with ENCODE", "my data is in mm9, how do I convert to mm10?"

Guide coordinate liftover between genome assemblies using UCSC liftOver, CrossMap, Ensembl REST API, and rtracklayer. Assembly conversion is one of the most common pitfalls in genomics — this skill provides the definitive workflow for safe, reproducible liftover with full provenance tracking.

## Scientific Rationale

**The question**: "How do I safely convert my genomic coordinates from one assembly to another without losing data or introducing errors?"
…

Read the whole file at its exact version.

How to install

The exact contents, by fingerprint

mdr add ammawla/encode-toolkit/liftover-coordinates@sha256:e6e734fd1df0b8ce

The line at the top of this page pins the label git:20260920.6050003, 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.

Badge

[![mdr](https://markdownregistry.com/badge/art_xe6yoqthfb2p7ubq.svg)](https://markdownregistry.com/a/art_xe6yoqthfb2p7ubq)

3 badge image fetches in 30 days. What the badge shows.

Versions

The registry has recorded 3 versions of this file, between Mar 12, 2026 and Sep 20, 2026, about one every 96 days.

version	committed	commit	size	audit
git:20260920.6050003 latest	2026-09-20	6050003	23,330 B	A	view · diff
git:20260920.ce7840d	2026-09-20	ce7840d	22,954 B	A	view · diff
git:20260312.665e731	2026-03-12	665e731	22,928 B	A	view

Audit of the latest version

A 17 of 17 checks passed. Fixed automatic checks with no AI involved, so the same checks give the same answer every run.

pass: Frontmatter block present
pass: Frontmatter declares a name
pass: Frontmatter declares a description
pass: Size between 200 bytes and 200 KB (23330 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

GitHub

ammawla/encode-toolkit · 21 stars · license AGPL-3.0 · pushed 2026-09-27 · branch main

API

GET https://markdownregistry.com/api/v1/artifacts/art_xe6yoqthfb2p7ubq
GET https://markdownregistry.com/api/v1/resolve?ref=ammawla/encode-toolkit/liftover-coordinates
GET https://markdownregistry.com/api/v1/blob/e6e734fd1df0b8ce0d41763649ecf0e50b8f050278acba35acfa44c3c83281d0

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.

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