Agent skill

Variant Analysis Tools

Variant and VCF workflow guide for local SNV, indel, and structural-variant summarization, filtering, and consequence triage.

Apache-2.0Auto-check passedResearch & Science

Install Variant Analysis Tools

skills CLI

$ npx skills add DrugClaw/DrugClaw --skill variant-analysis-tools -a claude-code

Project install by default; add -g for ~/.claude/skills/.

GitHub CLI

$ gh skill install DrugClaw/DrugClaw variant-analysis-tools --agent claude-code

Project scope by default; add --scope user for a personal install. Needs GitHub CLI 2.90.0 or later (public preview).

Manual copy

$ git clone --depth 1 https://github.com/DrugClaw/DrugClaw.git skills-src && mkdir -p .claude/skills && cp -r skills-src/skills/genomics/variant-analysis-tools .claude/skills/variant-analysis-tools && rm -rf skills-src

Use ~/.claude/skills/ instead of .claude/skills for a personal install. The folder must contain SKILL.md.

Claude Code skills documentation · loads skills from .claude/skills/

Paste into Claude Code

Install the "variant-analysis-tools" agent skill from https://github.com/DrugClaw/DrugClaw/tree/main/skills/genomics/variant-analysis-tools into .claude/skills/variant-analysis-tools/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "variant-analysis-tools", then confirm the skill loads.

Claude Code copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.

$skill-installer

$skill-installer install https://github.com/DrugClaw/DrugClaw/tree/main/skills/genomics/variant-analysis-tools

Type this inside Codex. $skill-installer <name> installs a curated skill from openai/skills. The installer writes to $CODEX_HOME/skills (default ~/.codex/skills). Restart Codex if the skill does not show up.

skills CLI

$ npx skills add DrugClaw/DrugClaw --skill variant-analysis-tools -a codex

Project install goes to .agents/skills/; add -g for ~/.codex/skills/.

GitHub CLI

$ gh skill install DrugClaw/DrugClaw variant-analysis-tools --agent codex

Project scope by default (.agents/skills/); add --scope user for a personal install.

Manual copy

$ git clone --depth 1 https://github.com/DrugClaw/DrugClaw.git skills-src && mkdir -p .agents/skills && cp -r skills-src/skills/genomics/variant-analysis-tools .agents/skills/variant-analysis-tools && rm -rf skills-src

Use ~/.agents/skills/ instead of .agents/skills for a personal install.

Codex skills documentation · loads skills from .agents/skills/

Paste into Codex

Install the "variant-analysis-tools" agent skill from https://github.com/DrugClaw/DrugClaw/tree/main/skills/genomics/variant-analysis-tools into .agents/skills/variant-analysis-tools/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "variant-analysis-tools", then confirm the skill loads.

Codex copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.

skills CLI

$ npx skills add DrugClaw/DrugClaw --skill variant-analysis-tools -a cursor

Project install goes to .agents/skills/; add -g for ~/.cursor/skills/.

GitHub CLI

$ gh skill install DrugClaw/DrugClaw variant-analysis-tools --agent cursor

Project scope by default (.agents/skills/); add --scope user for a personal install.

Manual copy

$ git clone --depth 1 https://github.com/DrugClaw/DrugClaw.git skills-src && mkdir -p .cursor/skills && cp -r skills-src/skills/genomics/variant-analysis-tools .cursor/skills/variant-analysis-tools && rm -rf skills-src

Use ~/.cursor/skills/ instead of .cursor/skills for a personal install.

Cursor skills documentation · loads skills from .cursor/skills/, .agents/skills/, .claude/skills/, .codex/skills/

Paste into Cursor

Install the "variant-analysis-tools" agent skill from https://github.com/DrugClaw/DrugClaw/tree/main/skills/genomics/variant-analysis-tools into .cursor/skills/variant-analysis-tools/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "variant-analysis-tools", then confirm the skill loads.

Cursor copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.

gemini skills install

$ gemini skills install https://github.com/DrugClaw/DrugClaw.git --path skills/genomics/variant-analysis-tools

--scope user (default) or --scope workspace; --path is the subfolder of the repo that holds the skill; --consent skips the security confirmation prompt.

skills CLI

$ npx skills add DrugClaw/DrugClaw --skill variant-analysis-tools -a gemini-cli

Project install goes to .agents/skills/; add -g for ~/.gemini/skills/.

GitHub CLI

$ gh skill install DrugClaw/DrugClaw variant-analysis-tools --agent gemini-cli

Project scope by default (.agents/skills/); add --scope user for a personal install.

Manual copy

$ git clone --depth 1 https://github.com/DrugClaw/DrugClaw.git skills-src && mkdir -p .gemini/skills && cp -r skills-src/skills/genomics/variant-analysis-tools .gemini/skills/variant-analysis-tools && rm -rf skills-src

Use ~/.gemini/skills/ instead of .gemini/skills for a personal install, then run /skills reload.

Gemini CLI skills documentation · loads skills from .gemini/skills/, .agents/skills/

Paste into Gemini CLI

Install the "variant-analysis-tools" agent skill from https://github.com/DrugClaw/DrugClaw/tree/main/skills/genomics/variant-analysis-tools into .gemini/skills/variant-analysis-tools/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "variant-analysis-tools", then confirm the skill loads.

Gemini CLI copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.

GitHub CLI

$ gh skill install DrugClaw/DrugClaw variant-analysis-tools

Installs for Copilot at project scope by default; add --scope user for a personal install. Preview a skill first with gh skill preview. Needs GitHub CLI 2.90.0 or later (public preview).

skills CLI

$ npx skills add DrugClaw/DrugClaw --skill variant-analysis-tools -a github-copilot

Project install goes to .agents/skills/; add -g for ~/.copilot/skills/.

Manual copy

$ git clone --depth 1 https://github.com/DrugClaw/DrugClaw.git skills-src && mkdir -p .github/skills && cp -r skills-src/skills/genomics/variant-analysis-tools .github/skills/variant-analysis-tools && rm -rf skills-src

Use ~/.copilot/skills/ instead of .github/skills for a personal install. Commit .github/skills so cloud agent and code review can use it.

GitHub Copilot skills documentation · loads skills from .github/skills/, .claude/skills/, .agents/skills/

Paste into GitHub Copilot

Install the "variant-analysis-tools" agent skill from https://github.com/DrugClaw/DrugClaw/tree/main/skills/genomics/variant-analysis-tools into .github/skills/variant-analysis-tools/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "variant-analysis-tools", then confirm the skill loads.

GitHub Copilot copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.

skills CLI

$ npx skills add DrugClaw/DrugClaw --skill variant-analysis-tools -a opencode

OpenCode documents no install command of its own. Project install goes to .agents/skills/; add -g for ~/.config/opencode/skills/.

GitHub CLI

$ gh skill install DrugClaw/DrugClaw variant-analysis-tools --agent opencode

Project scope by default (.agents/skills/); add --scope user for a personal install.

Manual copy

$ git clone --depth 1 https://github.com/DrugClaw/DrugClaw.git skills-src && mkdir -p .opencode/skills && cp -r skills-src/skills/genomics/variant-analysis-tools .opencode/skills/variant-analysis-tools && rm -rf skills-src

Use ~/.config/opencode/skills/ instead of .opencode/skills for a personal install.

OpenCode skills documentation · loads skills from .opencode/skills/, .claude/skills/, .agents/skills/

Paste into OpenCode

Install the "variant-analysis-tools" agent skill from https://github.com/DrugClaw/DrugClaw/tree/main/skills/genomics/variant-analysis-tools into .opencode/skills/variant-analysis-tools/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "variant-analysis-tools", then confirm the skill loads.

OpenCode copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.

Facts

Skill name: variant-analysis-tools
GitHub stars: 125
Token cost: ~722 tokens
SKILL.md length: 236 words
Files: 2
Skills in repo: 25
Repo updated: Mar 23, 2026
First seen: Oct 7, 2026
Licence: Apache-2.0

At a glance

Variant and VCF workflow guide for local SNV, indel, and structural-variant summarization, filtering, and consequence triage.

Works in 5 steps: Confirm which sample to read when the… → Decide whether the user wants raw… → Apply explicit filters for VAF, depth,… → …
The user asks to inspect a VCF
SKILL.md covers Environment Check, Bundled Asset, Preferred Workflow and Quick Start, plus 2 more sections
Runs Python scripts from its folder; calls python3

What it does

Variant Analysis Tools is an agent skill from DrugClaw/DrugClaw. Variant and VCF workflow guide for local SNV, indel, and structural-variant summarization, filtering, and consequence triage. Use when the user asks to inspect a VCF, count mutation classes, filter by VAF or depth, summarize genes or consequences, or prepare a local variant report before downstream annotation.

Its SKILL.md is about 720 tokens, which your agent loads only when the skill is triggered. The skill folder holds 2 other files (for example `templates/variant_report.py`).

It sits in Research & Science, covering Summarization and Bioinformatics. The repository describes itself as: 💊 AI Research Assistant for Accelerated Drug Discovery. 🦞. The licence is Apache-2.0.

When your agent uses it

The user asks to inspect a VCF
Count mutation classes
Summarize genes
Prepare a local variant report before downstream annotation

Example prompts

“/variant-analysis-tools”

Requirements

Python 3

Workflow steps

5 steps, taken from the first numbered list in SKILL.md.

Confirm which sample to read when the VCF is multi-sample.
Decide whether the user wants raw counts, filtered rows, or both.
Apply explicit filters for VAF, depth, PASS status, and consequence terms.
Export the filtered table plus a summary JSON.
If the user wants clinical significance or population frequency, hand the filtered rows to bio-db-tools for ClinVar, gnomAD, or dbSNP…

What it can do on your machine

Read from SKILL.md and the folder at commit 960a6e0. It shows what the files ask for, not the result of running them.

Tool permissions
Pre-approves nothing: there is no allowed-tools line, so your agent's usual permission prompts apply.
From allowed-tools in the SKILL.md frontmatter.
Runs code
Ships script files (Python), which the agent can run.
Shell commands in SKILL.md call:
- python3
From the folder's file list and the shell code blocks in SKILL.md.
Network
No URLs in SKILL.md.
From URLs in SKILL.md, links to its own repository left out.
Credentials
Names no API keys, tokens, secrets or passwords.
From names ending in _API_KEY, _TOKEN, _SECRET, _KEY or _PASSWORD in SKILL.md.

Context cost

Variant Analysis Tools loads about 722 tokens when it runs. Until then it costs about 84 tokens; SKILL.md has 236 words of instructions outside code blocks.

Always · name and description, kept in context so the agent knows when to use it: ~84
When it runs · the whole SKILL.md, loaded when a task matches: ~722

Estimates: characters ÷ 4, the usual rule of thumb; real counts depend on the model's tokenizer. Scripts and assets cost tokens only if the agent reads them.

Safety

Auto-check passed

The automated check found no risky patterns in SKILL.md.

Automated static check — not a guarantee. Review scripts before installing. It scans the text of SKILL.md for risky patterns (piping downloads into a shell, reading credential files, hidden Unicode, destructive commands); files beside SKILL.md are not scanned.

SKILL.md

The full file from DrugClaw/DrugClaw at commit 960a6e0, republished under its Apache-2.0 licence (© DrugClaw). 236 words, ~722 tokens.

Download SKILL.mdSave it as .claude/skills/variant-analysis-tools/SKILL.md (or your agent's skills folder). This skill also uses 1 other file; get the full folder from GitHub.

name: variant-analysis-tools
description: Variant and VCF workflow guide for local SNV, indel, and structural-variant summarization, filtering, and consequence triage. Use when the user asks to inspect a VCF, count mutation classes, filter by VAF or depth, summarize genes or consequences, or prepare a local variant report before downstream annotation.
source: drugclaw
updated_at: 2026-03-11

Variant Analysis Tools

Use this skill when the user provides a VCF or BCF and wants concrete counts, filtering, or mutation summaries instead of only database lookup.

Typical triggers:

summarize the contents of a VCF or BCF
count SNVs, indels, or structural variants
filter by VAF, read depth, PASS status, or variant type
exclude intronic or intergenic consequences from a local callset
generate a machine-readable variant table before ClinVar, gnomAD, or dbSNP follow-up

Environment Check

bash

which python3 || true
python3 - <<'PY'
mods = ["pysam"]
for name in mods:
    try:
        __import__(name)
        print(f"{name}: ok")
    except Exception as exc:
        print(f"{name}: missing ({exc})")
PY

Do not claim VCF analysis ran if pysam is unavailable.

Bundled Asset

templates/variant_report.py

Preferred Workflow

Confirm which sample to read when the VCF is multi-sample.
Decide whether the user wants raw counts, filtered rows, or both.
Apply explicit filters for VAF, depth, PASS status, and consequence terms.
Export the filtered table plus a summary JSON.
If the user wants clinical significance or population frequency, hand the filtered rows to bio-db-tools for ClinVar, gnomAD, or dbSNP follow-up.

Quick Start

bash

python3 templates/variant_report.py \
  --input cohort/sample.vcf.gz \
  --sample TUMOR \
  --pass-only \
  --min-vaf 0.05 \
  --min-depth 20 \
  --exclude-consequence intronic \
  --exclude-consequence intergenic \
  --output variants/sample_filtered.csv \
  --summary variants/sample_filtered.json

Structural-variant focused example:

bash

python3 templates/variant_report.py \
  --input sv_calls.vcf.gz \
  --include-variant-type DEL \
  --include-variant-type DUP \
  --output variants/sv_subset.csv \
  --summary variants/sv_subset.json

Output Expectations

Good answers should mention:

the exact variant file and sample used
which filters were applied
total records seen versus retained
variant-type and consequence distributions
top affected genes after filtering
where the CSV and summary JSON were written

For ClinVar, Ensembl, gnomAD, or dbSNP lookups, activate bio-db-tools. For statistical testing or survival modeling on variant-derived burden tables, activate stat-modeling-tools or survival-analysis-tools. For target-level interpretation around genes hit by the variants, activate target-intelligence-tools.

Files

SKILL.md and 1 other file in skills/genomics/variant-analysis-tools of DrugClaw/DrugClaw.

SKILL.md
templates/variant_report.py

Open the folder on GitHubat commit 960a6e0

Compare with similar skills

Variant Analysis Tools next to the 5 skills that share the most tags, products or categories with it. Stars are the repository's; “used in” counts other GitHub owners with a copy.

Variant Analysis Tools compared with similar skills
Skill	Stars	Used in	Tokens	Auto-check	Licence	Repo updated
Variant Analysis Tools this skillDrugClaw/DrugClaw	125	—	~722	Automated safety check: Pass	Apache-2.0	6 mo ago
Bio Phylo Bayesian InferenceGPTomics/bioSkills	1.2k	1 repos	~6.9k	Automated safety check: Pass	MIT	1 mo ago
Bioconductor MsstatslipbioMate-AI/biomate-bioconductor-kb	804	—	~1.1k	Automated safety check: Pass	Custom licence	3 mo ago
Bio Proteomics QuantificationGPTomics/bioSkills	1.2k	1 repos	~5.9k	Automated safety check: Pass	MIT	1 mo ago
Rebuttal ResponseM1n-n9/paper-lifecycle	692	—	~1.9k	Automated safety check: Pass	None	3 mo ago
Daily Paper DigestGalaxy-Dawn/claude-scholar	5.7k	—	~1k	Automated safety check: Pass	MIT	16 days ago

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Questions about Variant Analysis Tools

What does Variant Analysis Tools do?

Variant and VCF workflow guide for local SNV, indel, and structural-variant summarization, filtering, and consequence triage. Variant Analysis Tools is an agent skill from DrugClaw/DrugClaw. Variant and VCF workflow guide for local SNV, indel, and structural-variant summarization, filtering, and consequence triage.

When should I use Variant Analysis Tools?

Variant Analysis Tools fits situations like: the user asks to inspect a VCF; count mutation classes; summarize genes; prepare a local variant report before downstream annotation.

How do I install Variant Analysis Tools in Claude Code?

Run `npx skills add DrugClaw/DrugClaw --skill variant-analysis-tools -a claude-code`. Or copy the skill folder (skills/genomics/variant-analysis-tools in DrugClaw/DrugClaw) into .claude/skills/variant-analysis-tools in your project. Claude Code loads it when a task matches its description.

How do I install Variant Analysis Tools in Codex?

Run `npx skills add DrugClaw/DrugClaw --skill variant-analysis-tools -a codex`. Or copy the skill folder (skills/genomics/variant-analysis-tools in DrugClaw/DrugClaw) into .agents/skills/variant-analysis-tools in your project. Codex loads it when a task matches its description.

Can I use Variant Analysis Tools in Cursor, Gemini CLI or GitHub Copilot?

Cursor, Gemini CLI, GitHub Copilot and OpenCode also load SKILL.md folders. With the skills CLI, run `npx skills add DrugClaw/DrugClaw --skill variant-analysis-tools -a cursor` (or -a gemini-cli, github-copilot or opencode for the others). To copy it by hand, put the folder in .cursor/skills/variant-analysis-tools, .gemini/skills/variant-analysis-tools, .github/skills/variant-analysis-tools and .opencode/skills/variant-analysis-tools in your project.

What does Variant Analysis Tools need to run?

Going by SKILL.md and its folder, Variant Analysis Tools needs Python for the scripts in its folder and the command-line tools its instructions call (python3). Our summary lists: Python 3.

Does Variant Analysis Tools access the network?

SKILL.md contains no URLs. Any network use would come from the scripts or tools the agent runs. This is read from the text; nothing was executed.

Is Variant Analysis Tools safe to install?

Our automated static check of SKILL.md found no risky patterns, such as piping downloads into a shell, reading credential files or hidden Unicode. It is not a guarantee. Review the folder before installing.

What licence does Variant Analysis Tools use?

Variant Analysis Tools is published under the Apache-2.0 licence (the repository's licence). It allows redistribution, so the full SKILL.md is shown on this page.

How many tokens does Variant Analysis Tools use?

About 722 tokens (SKILL.md is roughly 2.9k characters). Agents keep only the skill's name and description in context until a task matches; then they load SKILL.md in full.

What are the alternatives to Variant Analysis Tools?

Skills that share tags, products or a category with Variant Analysis Tools: Bio Phylo Bayesian Inference (GPTomics/bioSkills, 1.2k stars), Bioconductor Msstatslip (bioMate-AI/biomate-bioconductor-kb, 804 stars), Bio Proteomics Quantification (GPTomics/bioSkills, 1.2k stars) and Rebuttal Response (M1n-n9/paper-lifecycle, 692 stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.

Who maintains Variant Analysis Tools?

DrugClaw (a GitHub organization) maintains it in DrugClaw/DrugClaw, which has 125 GitHub stars. The repository holds 25 skills in this directory. The repository was last updated on March 23, 2026.

Source: DrugClaw/DrugClaw on GitHub. Facts on this page come from the repository at the commit we read; the author's words are quoted as theirs.

Variant Analysis Tools

Install Variant Analysis Tools

Facts

At a glance

What it does

When your agent uses it

Example prompts

Requirements

Workflow steps

What it can do on your machine

Tool permissions

Runs code

Network

Credentials

Context cost

Safety

SKILL.md

Variant Analysis Tools

Environment Check

Bundled Asset

Preferred Workflow

Quick Start

Output Expectations

Files

Compare with similar skills

Similar skills

Bio Phylo Bayesian Inference

Bioconductor Msstatslip

Bio Proteomics Quantification

Rebuttal Response

Daily Paper Digest

Literature Synthesis Guide

More from DrugClaw/DrugClaw

Bio DB Tools

Grn Tools

Knowledge Graph Tools

Literature Review Tools

Medical Data Tools

Omics Tools

Questions about Variant Analysis Tools

Install Variant Analysis Tools

Facts

At a glance

What it does

When your agent uses it

Example prompts

Requirements

Workflow steps

What it can do on your machine

Tool permissions

Runs code

Network

Credentials

Context cost

Safety

SKILL.md

Variant Analysis Tools

Environment Check

Bundled Asset

Preferred Workflow

Quick Start

Output Expectations

Related Skills

Files

Compare with similar skills

Similar skills

More from DrugClaw/DrugClaw

Related

Questions about Variant Analysis Tools