snpeff-variant-annotation SKILL.md skillA
snpeff-variant-annotation from jaechang-hits/sciagent-skills is an agent skill: a SKILL.md folder an AI agent loads when a task calls for it.
mdr add jaechang-hits/sciagent-skills/snpeff-variant-annotation@git:20260929.7a7d60fPins git:20260929.7a7d60f in mdr.lock. Pin the fingerprint instead.
- Audit grade
- A, 17 of 17 checks passed
- Kind
- SKILL.md skill
- Repository
- jaechang-hits/sciagent-skills
- Path
skills/genomics-bioinformatics/variant/snpeff-variant-annotation/SKILL.md- Versions recorded
- 4
- Latest version
- git:20260929.7a7d60f, committed Sep 29, 2026
- First version recorded
- May 28, 2026
- Size
- 21,768 bytes
- Repository stars
- 381
- License
- a license file GitHub does not identify
Annotate and filter VCF variants with SnpEff and SnpSift. SnpEff predicts functional effects (HIGH/MODERATE/LOW/MODIFIER), genes, transcripts, AA changes, HGVS; SnpSift filters and adds ClinVar/dbSNP. Java CLI with Python subprocess integration. Use ANNOVAR for multi-database annotation; Ensembl VEP for REST API; SnpEff for fast CLI with pre-built genomes.
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
# SnpEff + SnpSift — Variant Annotation and Filtering ## Overview SnpEff annotates variants in VCF files by predicting their functional consequences: impact level (HIGH, MODERATE, LOW, MODIFIER), affected gene and transcript, amino acid change, and HGVS notation. SnpSift is the companion tool for filtering, sorting, and enriching annotated VCFs with external databases such as ClinVar and dbSNP. Together they form a fast, self-contained pipeline for going from raw variant calls to biologically interpretable, filtered variant sets. Both tools are Java-based and are invoked from the command line or Python subprocess; pre-built genome databases (hg38, GRCh37, mm10, and 100+ others) are downloaded with a single command. ## When to Use - Annotating VCF files from GATK, DeepVariant, bcftools, or other callers with predicted gene-level functional consequences before manual review or downstream filtering - Prioritizing clinically relevant variants by filtering to HIGH-impact stop-gain, frameshift, and splice-site variants for rare disease or cancer gene panel analysis …
Read the whole file at its exact version.
How to install
mdr add jaechang-hits/sciagent-skills/snpeff-variant-annotation@sha256:abd747c38783dc50The line at the top of this page pins the label git:20260929.7a7d60f, 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_hskztbylkzfzpfgu)
2 badge image fetches in 30 days. What the badge shows.
Versions
The registry has recorded 4 versions of this file, between May 28, 2026 and Sep 29, 2026, about one every 41 days.
| version | committed | commit | size | audit | |
|---|---|---|---|---|---|
| git:20260929.7a7d60f latest | 2026-09-29 | 7a7d60f | 21,768 B | A | view · diff |
| git:20260929.35fe6e3 | 2026-09-29 | 35fe6e3 | 21,817 B | A | view · diff |
| git:20260827.cbbeb75 | 2026-08-27 | cbbeb75 | 20,111 B | A | view · diff |
| git:20260528.3e3f998 | 2026-05-28 | 3e3f998 | 20,527 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 (21768 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
jaechang-hits/sciagent-skills · 381 stars · license a license file GitHub does not identify · pushed 2026-10-16 · branch main
API
GET https://markdownregistry.com/api/v1/artifacts/art_hskztbylkzfzpfgu GET https://markdownregistry.com/api/v1/resolve?ref=jaechang-hits/sciagent-skills/snpeff-variant-annotation GET https://markdownregistry.com/api/v1/blob/abd747c38783dc507c9be7511549e5697cb31da87df8d87907216880a8d4ccd8
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.