variant-annotation
Skill1 starsChanged 40 days agoNo licenceView on GitHub
Annotate and interpret human DNA variants (SNV, indel) — normalize VCF with bcftools norm (left-align, split multiallelics), convert rsID / HGVS / chr-pos-ref-alt with Ensembl variant_recoder, predict consequences with the Ensembl VEP REST API (GRCh38, GRCh37), look up ClinVar clinical significance and review status via NCBI E-utilities, get gnomAD population allele frequencies via the GraphQL API (gnomad_r4), read AlphaMissense and REVEL missense pathogenicity scores, and frame evidence under ACMG/AMP criteria (PM2, BA1, PP3, BP4; Pejaver 2022, Bergquist 2025 calibrations). Use for VUS triage, variant lookup, annotating a short variant list, benchmark-label provenance (ClinVar/predictor leakage). Research support only, not clinical classification. Not for variant calling or GWAS; not for genome-scale VCF annotation (run local VEP/bcftools csq instead).
2 other projects use a version of this.
Adopted by
Most recently taken up by
- zamushwani/biomedical-ai-skillstheir own version, first seen Aug 26, 2026
- ammawla/encode-toolkittheir own version, first seen Mar 8, 2026
Other versions2 projects use a version of this.
Word for word · 0
None found.
Edited · 0
None found.
Wrote their own version · 2
- ammawla/encode-toolkit★ 20same name
- zamushwani/biomedical-ai-skills★ 1same name
How matches are found. Word for word: the exact same text. Edited: shares passages with this file (“99% same” means 99% of its five-word phrases also appear here; 10% or more counts). Their own version: similar meaning, or, weakest, the same name. We can’t tell which project had it first. Projects are counted among the 200 most-starred candidates, and mentions are links to the repository we found, up to 50 per site, so both counts are a floor.
In this repository23 other files it gives its agents.
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- deslopSkill
- doc-build-gateSkill
- experiment-preflight-singlecellSkill
- experiment-preflightSkill
- fail-loud-pipelinesSkill
- gwas-analysisSkill
- job-watchSkill
- lab-notebookSkill
- paper-outlineSkill
- phase-delegationSkill
- reproducibleSkill
- rigor-reviewSkill
- run-status-boardSkill
- science-daemon-opsSkill
- session-handoffSkill
- standing-instructionsSkill
- variant-callingSkill
The file
We split this skill into the rules it gives an agent
2 rules. About 0 are common, 1 is distinctive, and 1 is very specific to this project.
≈0
Common · estimate
Many files like this have a rule of this kind.
≈1
Distinctive · estimate
This author's own choices. Worth a look.
1
Very specific
Tied to their project's names, files or tools. Probably skip.
No licence file, so all rights are reserved — read it at the source. We count its rules but don't quote them. Read them on GitHub.
≈ “Common” is an estimate: at least 1 in 5 of the 350,495 skill files we read have a rule of the same kind, not the same words. “Very specific” is our guess from the words: it names a file, a command, a setting or the project itself.
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