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annotate-variants

annotate-variants is a command for Claude Code from zamushwani/biomedical-ai-skills. It costs 0 tokens per session (374 once invoked), scanned A, original, MIT.

A command for annotating genetic variants from a VCF, a file containing DNA variant calls, and interpreting their clinical meaning for a specified tumour type.

In plain words
What is it for?
Use it to normalize variants, annotate their gene effects, classify germline or somatic significance, assign tumour-specific clinical tiers, and report supporting evidence.
Why use it?
It separates variant normalization, functional annotation, cancer-driving potential, and treatment relevance so these different judgments are not confused.

Command for Claude Code

Written for Claude Code: allowed-tools in frontmatter. Also seen: positional $N argument.

not rated 1repo 1mo ago A scan 0 tokens original MIT

Good fit Use it to normalize variants, annotate their gene effects, classify germline or somatic significance, assign tumour-specific clinical tiers, and report supporting evidence.

Compare 6 commands from other repositories ↓
Install with agentmods
npx agentmods add commands/zamushwani/biomedical-ai-skills/annotate-variants
View source ↗ zamushwani/biomedical-ai-skills
Install

Getting it into your agent

One page per mod, every tool's command on it. A separate URL per tool would split the same page into five that compete with each other.

Clone the repo
git clone --depth 1 https://github.com/zamushwani/biomedical-ai-skills

Made for: Claude Code.

Wrote this? Show the measurements

A badge with what this costs and how it scanned, read live from this page, so it follows the numbers instead of freezing them. Markdown for a README, HTML for a documentation site or a project page.

agentmods badge for annotate-variants

README.md
[![agentmods](https://agentmods.dev/badge/commands/zamushwani/biomedical-ai-skills/annotate-variants/github.svg)](https://agentmods.dev/commands/zamushwani/biomedical-ai-skills/annotate-variants)
Your own site
<a href="https://agentmods.dev/commands/zamushwani/biomedical-ai-skills/annotate-variants"><img src="https://agentmods.dev/badge/commands/zamushwani/biomedical-ai-skills/annotate-variants/github.svg" alt="Measured on agentmods" height="20"></a>

Or the 80×15 button, for a site that already has a row of RSS and ATOM ones. Only the verdict fits; the numbers stay here.

agentmods 80×15 button for annotate-variants

Your own site · 80×15
<a href="https://agentmods.dev/commands/zamushwani/biomedical-ai-skills/annotate-variants"><img src="https://agentmods.dev/badge/commands/zamushwani/biomedical-ai-skills/annotate-variants.svg" alt="Reviewed on agentmods" width="80" height="20"></a>
Per session 0 Only the description is in the session, so the agent can decide to use it. The body loads when it is invoked.
When invoked 374 The whole file, excluding the scripts and references it only reads on demand.
Security scan A 0 findings. A grade says what 26 rules found in the file — not that it is safe.
Origin original No closer match found in the catalogue.
Token cost

What it costs to keep this loaded

Counted locally with the o200k_base tokenizer, which is exact for GPT models; Claude uses its own tokenizer and its counts differ. Treat this as one consistent yardstick across the catalogue rather than a bill. Prices are per million input tokens.

ModelPer sessionOnce invoked
Fable 5.1 $0.00000 $0.00374
Opus 5.5 $0.00000 $0.00150
Sonnet 5.5 $0.00000 $0.00075
Haiku 4.5 $0.00000 $0.00037

Measured 2mo ago against content hash 2b2f6133ca7e, method: parsed. Prices are Anthropic first-party input rates as of 2026-10-07, from the pricing page.

Security

Grade A, and why

annotate-variants scanned grade A with 0 findings against 26 rules in 11 categories — prompt injection, anti-refusal, data exfiltration, privilege escalation, supply chain, agent snooping, system-prompt leakage, SSRF and excessive agency — measured 2mo ago.

A static scan of the body, not an audit. Every finding is printed with the line that produced it so you can judge whether it matters here. A mod is markdown that instructs an agent; that is exactly why what it instructs is worth reading.

Nothing flagged

None of the 26 patterns this scan looks for appear in this file: no shell pipes, no recursive deletes, no credential paths, no hidden text, no instruction-override or anti-refusal phrasing, no agent-config snooping. That is not a guarantee, it is the absence of the things that are checkable.

.claude/commands/annotate-variants.md · 27 lines

What it actually says

Annotate the variants in $0 for tumour type $1.

Follow the variant-annotation skill. Order matters:

  1. Normalize first: bcftools norm -m -any -f <ref>. Un-normalized records fail knowledgebase lookups silently — the variant reads as absent, not as an error.
  2. Then annotate (VEP/SnpEff), picking the transcript-selection rule deliberately and stating it.
  3. Then classify on the right axis. These are three separate frameworks:
ACMG/AMP 2015          germline pathogenicity      germline only
ClinGen/CGC/VICC 2022  somatic oncogenicity        is it driving?
AMP/ASCO/CAP 2017      clinical tiers              does it change management?

Oncogenicity and actionability are different axes: KRAS G12D is unambiguously oncogenic and can still be Tier III where nothing acts on it.

  1. A tier requires a tumour type. BRAF V600E is Tier IA in melanoma and Tier IIC in colorectal. If $1 is empty, ask for it — do not assign tiers without it.
  2. Use popmax, not global, allele frequency. 0.1% globally can be 4% in one ancestry group.

Report per variant: gene, HGVS, consequence, population AF (popmax), classification with the criteria applied, and the evidence source.

Changes

What this file has done since we first saw it

Hashed on every crawl. A supply-chain change to an agent config is a question of when, not whether, so the history is kept rather than the latest state alone.

  1. 2mo ago First seen · 27 lines · 0 tokens per session scan A 2b2f6133ca7e

Subscribe to this mod's changes

annotate-variants is a command published in the GitHub repository zamushwani/biomedical-ai-skills (1 stars, last pushed 1mo ago), licensed MIT. It costs nothing until one of its globs matches a file; then it loads 374 tokens. A static security scan graded it A with 0 findings. No closer match exists in the catalogue, so it is treated as the original; first seen 2026-08-31.

DESeq2Scientificai-agentai-skillsbioinformaticscancer-genomicscancer-research
Related

annotate-variants compared with commands from other repositories

annotate-variants next to 6 commands from other repositories
ModTypeStarsLast pushLicenceScanTokensWorks with
annotate-variantszamushwani/biomedical-ai-skillsCommand11mo agoMITA0Claude Code
readaipoch/medical-research-skillsCommand2.0k1mo agoMITA0Claude Code
feedaipoch/medical-research-skillsCommand2.0k1mo agoMITA0Claude Code
annotateHERRY423/CellTypePilotCommand62mo agoMITA16Claude Code
criticHERRY423/CellTypePilotCommand62mo agoMITA14Claude Code
ctp-inspectHERRY423/CellTypePilotCommand62mo agoMITA16Claude Code
faostat-country-profileberba-q/faostat-skillsCommand106mo agoMITA10Claude Code