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variant-annotation SKILL.md skillA

variant-annotation 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/variant-annotation@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/variant-annotation/SKILL.md
Versions recorded: 4
Latest version: git:20260920.6050003, committed Sep 20, 2026
First version recorded: Mar 12, 2026
Size: 29,830 bytes
Repository stars: 21
License: AGPL-3.0

Annotate genetic variants (GWAS hits, eQTLs, rare variants) with ENCODE functional data to interpret non-coding variation. Use when the user has variants of interest and wants to understand their regulatory context, identify causal variants from GWAS loci, assess variant impact on regulatory elements, perform enrichment testing of variant sets in tissue-specific annotations, or link variants to target genes through enhancer-gene maps. Handles the full post-GWAS workflow from variant set →…

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

# Functional Annotation of Genetic Variants with ENCODE Data

## When to Use

- User wants to annotate genetic variants with ENCODE regulatory element overlap and functional evidence
- User asks about "variant annotation", "regulatory variants", "non-coding variants", or "variant prioritization"
- User needs to assess whether a variant falls in an active enhancer, promoter, or TF binding site
- User wants to build a multi-evidence variant interpretation combining ENCODE + ClinVar + gnomAD
- Example queries: "annotate my GWAS hits with ENCODE regulatory data", "does this variant disrupt a TF binding site?", "prioritize non-coding variants by regulatory impact"

Interpret non-coding genetic variation by layering ENCODE functional genomics annotations to identify causal regulatory variants and link them to target genes.

## Scientific Rationale

**The question**: "Which of my GWAS/eQTL variants actually disrupt regulatory elements, and what genes do they affect?"
…

Read the whole file at its exact version.

How to install

The exact contents, by fingerprint

mdr add ammawla/encode-toolkit/variant-annotation@sha256:355c7f451018a9bc

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_shayhrrhpjefl2jr.svg)](https://markdownregistry.com/a/art_shayhrrhpjefl2jr)

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

Versions

The registry has recorded 4 versions of this file, between Mar 12, 2026 and Sep 20, 2026, about one every 64 days.

version	committed	commit	size	audit
git:20260920.6050003 latest	2026-09-20	6050003	29,830 B	A	view · diff
git:20260920.ce7840d	2026-09-20	ce7840d	29,365 B	A	view · diff
git:20260321.d9029d0	2026-03-21	d9029d0	29,349 B	A	view · diff
git:20260312.be32706	2026-03-12	be32706	29,343 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 (29830 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_shayhrrhpjefl2jr
GET https://markdownregistry.com/api/v1/resolve?ref=ammawla/encode-toolkit/variant-annotation
GET https://markdownregistry.com/api/v1/blob/355c7f451018a9bc4a0cc31ff9b505553d9459d6bd11a539eec8206d993817e3

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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