liftover-coordinates skillA
liftover-coordinates is agent-read markdown (skill) from ammawla/encode-toolkit: 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..
Indexed from public GitHub and served as immutable, content-addressed versions. Install it pinned to an exact SHA-256 with the mdr CLI, and every file is verified against the hash recorded here before it reaches your agent. The deterministic audit below grades the latest version, and the same file always earns 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?" …
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How to install
mdr add ammawla/encode-toolkit/liftover-coordinates@git:20260312.665e731mdr add ammawla/encode-toolkit/liftover-coordinates@sha256:449b89d26da4b1e8Pin to a label to follow the author's releases, or to a sha256 to freeze the exact bytes forever. Either way the resolved hash is written to mdr.lock, and mdr install reproduces it on any machine.
[](https://markdownregistry.com/a/art_xe6yoqthfb2p7ubq)
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Versions
Audit of the latest version
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- 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
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Source
ammawla/encode-toolkit · 20 stars · license AGPL-3.0 · pushed 2026-09-21 · 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/449b89d26da4b1e8be03cc73cffa0124175e8e5a900faa2d37428c30127669f1
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