Alphagenome Single Variant Analysis
google-deepmind/science-skills
Analyzes genetic variant effects on gene expression (RNA-seq), chromatin accessibility (DNASE), histone marks (ChIP), and transcription factors using the AlphaGenome API.
Load when summarising / filtering a VCF — variant classification (SNP / MNP / INS / DEL / COMPLEX), Ti/Tv ratio, QUAL / DP threshold filtering, INFO-field parsing.
Install Genomics Vcf Operations
$ npx skills add TianGzlab/OmicsClaw --skill genomics-vcf-operations -a claude-codeProject install by default; add -g for ~/.claude/skills/.
$ gh skill install TianGzlab/OmicsClaw genomics-vcf-operations --agent claude-codeProject scope by default; add --scope user for a personal install. Needs GitHub CLI 2.90.0 or later (public preview).
$ git clone --depth 1 https://github.com/TianGzlab/OmicsClaw.git skills-src && mkdir -p .claude/skills && cp -r skills-src/skills/genomics/genomics-vcf-operations .claude/skills/genomics-vcf-operations && rm -rf skills-srcUse ~/.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/
Install the "genomics-vcf-operations" agent skill from https://github.com/TianGzlab/OmicsClaw/tree/main/skills/genomics/genomics-vcf-operations into .claude/skills/genomics-vcf-operations/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "genomics-vcf-operations", 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 install https://github.com/TianGzlab/OmicsClaw/tree/main/skills/genomics/genomics-vcf-operationsType 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.
$ npx skills add TianGzlab/OmicsClaw --skill genomics-vcf-operations -a codexProject install goes to .agents/skills/; add -g for ~/.codex/skills/.
$ gh skill install TianGzlab/OmicsClaw genomics-vcf-operations --agent codexProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/TianGzlab/OmicsClaw.git skills-src && mkdir -p .agents/skills && cp -r skills-src/skills/genomics/genomics-vcf-operations .agents/skills/genomics-vcf-operations && rm -rf skills-srcUse ~/.agents/skills/ instead of .agents/skills for a personal install.
Codex skills documentation · loads skills from .agents/skills/
Install the "genomics-vcf-operations" agent skill from https://github.com/TianGzlab/OmicsClaw/tree/main/skills/genomics/genomics-vcf-operations into .agents/skills/genomics-vcf-operations/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "genomics-vcf-operations", 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.
$ npx skills add TianGzlab/OmicsClaw --skill genomics-vcf-operations -a cursorProject install goes to .agents/skills/; add -g for ~/.cursor/skills/.
$ gh skill install TianGzlab/OmicsClaw genomics-vcf-operations --agent cursorProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/TianGzlab/OmicsClaw.git skills-src && mkdir -p .cursor/skills && cp -r skills-src/skills/genomics/genomics-vcf-operations .cursor/skills/genomics-vcf-operations && rm -rf skills-srcUse ~/.cursor/skills/ instead of .cursor/skills for a personal install.
Cursor skills documentation · loads skills from .cursor/skills/, .agents/skills/, .claude/skills/, .codex/skills/
Install the "genomics-vcf-operations" agent skill from https://github.com/TianGzlab/OmicsClaw/tree/main/skills/genomics/genomics-vcf-operations into .cursor/skills/genomics-vcf-operations/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "genomics-vcf-operations", 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 https://github.com/TianGzlab/OmicsClaw.git --path skills/genomics/genomics-vcf-operations--scope user (default) or --scope workspace; --path is the subfolder of the repo that holds the skill; --consent skips the security confirmation prompt.
$ npx skills add TianGzlab/OmicsClaw --skill genomics-vcf-operations -a gemini-cliProject install goes to .agents/skills/; add -g for ~/.gemini/skills/.
$ gh skill install TianGzlab/OmicsClaw genomics-vcf-operations --agent gemini-cliProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/TianGzlab/OmicsClaw.git skills-src && mkdir -p .gemini/skills && cp -r skills-src/skills/genomics/genomics-vcf-operations .gemini/skills/genomics-vcf-operations && rm -rf skills-srcUse ~/.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/
Install the "genomics-vcf-operations" agent skill from https://github.com/TianGzlab/OmicsClaw/tree/main/skills/genomics/genomics-vcf-operations into .gemini/skills/genomics-vcf-operations/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "genomics-vcf-operations", 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.
$ gh skill install TianGzlab/OmicsClaw genomics-vcf-operationsInstalls 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).
$ npx skills add TianGzlab/OmicsClaw --skill genomics-vcf-operations -a github-copilotProject install goes to .agents/skills/; add -g for ~/.copilot/skills/.
$ git clone --depth 1 https://github.com/TianGzlab/OmicsClaw.git skills-src && mkdir -p .github/skills && cp -r skills-src/skills/genomics/genomics-vcf-operations .github/skills/genomics-vcf-operations && rm -rf skills-srcUse ~/.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/
Install the "genomics-vcf-operations" agent skill from https://github.com/TianGzlab/OmicsClaw/tree/main/skills/genomics/genomics-vcf-operations into .github/skills/genomics-vcf-operations/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "genomics-vcf-operations", 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.
$ npx skills add TianGzlab/OmicsClaw --skill genomics-vcf-operations -a opencodeOpenCode documents no install command of its own. Project install goes to .agents/skills/; add -g for ~/.config/opencode/skills/.
$ gh skill install TianGzlab/OmicsClaw genomics-vcf-operations --agent opencodeProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/TianGzlab/OmicsClaw.git skills-src && mkdir -p .opencode/skills && cp -r skills-src/skills/genomics/genomics-vcf-operations .opencode/skills/genomics-vcf-operations && rm -rf skills-srcUse ~/.config/opencode/skills/ instead of .opencode/skills for a personal install.
OpenCode skills documentation · loads skills from .opencode/skills/, .claude/skills/, .agents/skills/
Install the "genomics-vcf-operations" agent skill from https://github.com/TianGzlab/OmicsClaw/tree/main/skills/genomics/genomics-vcf-operations into .opencode/skills/genomics-vcf-operations/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "genomics-vcf-operations", 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
genomics-vcf-operations- GitHub stars
- 161
- Token cost
- ~1.1k tokens
- SKILL.md length
- 429 words
- Files
- 9 (incl. references)
- Skills in repo
- 88
- Repo updated
- First seen
- Licence
- Apache-2.0
At a glance
Load when summarising / filtering a VCF — variant classification (SNP / MNP / INS / DEL / COMPLEX), Ti/Tv ratio, QUAL / DP threshold filtering, INFO-field parsing.
- Tasks that involve Bioinformatics
- SKILL.md covers When to use, Use from a step, API and Methods and parameters, plus 5 more sections
- Runs Python scripts from its folder; calls python
What it does
Genomics Vcf Operations is an agent skill from TianGzlab/OmicsClaw. Load when summarising / filtering a VCF — variant classification (SNP / MNP / INS / DEL / COMPLEX), Ti/Tv ratio, QUAL / DP threshold filtering, INFO-field parsing. Skip when calling variants from BAM (run an external caller first); adding functional annotations (use genomics-variant-annotation).
Its SKILL.md is about 1.1k tokens, which your agent loads only when the skill is triggered. The skill folder holds 12 other files, including reference files (for example `_api.py`, `examples/example_step.py` and `genomics_vcf_operations.py`).
It sits in Research & Science, covering Bioinformatics. The repository describes itself as: Conversational & memory-enabled AI research partner for multi-omics analysis. CLI + Desktop App (installers in Releases). From biological idea to full research paper. The licence is Apache-2.0.
When your agent uses it
- Tasks that involve Bioinformatics
Example prompts
- “/genomics-vcf-operations”
Requirements
- Python 3
What it can do on your machine
Read from SKILL.md and the folder at commit 90a3bec. 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:
python
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
Genomics Vcf Operations loads about 1.1k tokens when it runs, and up to ~1.6k if it reads all its reference files. Until then it costs about 80 tokens; SKILL.md has 429 words of instructions outside code blocks.
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 TianGzlab/OmicsClaw at commit 90a3bec, republished under its Apache-2.0 licence (© TianGzlab). 429 words, ~1,135 tokens.
Download SKILL.mdSave it as
.claude/skills/genomics-vcf-operations/SKILL.md (or your agent's skills folder). This skill also uses 8 other files; get the full folder from GitHub.- name
- genomics-vcf-operations
- description
- Load when summarising / filtering a VCF — variant classification (SNP / MNP / INS / DEL / COMPLEX), Ti/Tv ratio, QUAL / DP threshold filtering, INFO-field parsing. Skip when calling variants from BAM (run an external caller first); adding functional annotations (use genomics-variant-annotation).
- trigger
- VCF, bcftools, variant filter, merge VCF
- tags
- genomics, vcf, bcftools, filter, ti-tv, snv, indel
genomics-vcf-operations
When to use
Load this skill for the file-based analysis named in the description. The function library and CLI share the same calculations; no external aligner, assembler, caller or annotation service is started.
Use from a step
from skills._sdk.notebook import load_skill, read_input, write_output
library = load_skill("genomics-vcf-operations")
data = read_input("input.vcf", reader=library.read_records)
result = library.analyze(data)
write_output(result, "tables/result.csv")
write_output(library.distribution_figure(result), "figures/distribution.png")Run examples/example_step.py through the step runner for a small,
hand-worked synthetic fixture. It asserts known summary values.
The reader materializes the input in memory; use bounded FASTQ reads or
pre-filter large genomic files before loading them.
API
<!-- api:begin generated from _api.py; regenerate with run.py api <skill dir> --write -->read_records(path: str | Path) -> pd.DataFrame
Read records through read_input(path, reader=library.read_records).
:param path: Input file in the format documented under Inputs and outputs.
:returns: Parsed records as a DataFrame. :raises ValueError: Input values or file structure cannot be parsed.
analyze(data: pd.DataFrame, *, min_qual: float=0.0, min_dp: int=0) -> pd.DataFrame
Compute vcf-operations summaries and return a new table, leaving data unchanged.
:param data: Records containing chrom, pos, ref, alt, qual, filter, dp, type. :param min_qual: CLI default 0 keeps all QUAL values; raise to filter. :param min_dp: CLI default 0 keeps all INFO/DP values; FORMAT/DP is ignored. :returns: Result table with diagnostics and summary in attrs['run_info']. :raises ValueError: Required columns are absent or records are empty or invalid.
run_info(data: pd.DataFrame, *, keep: bool=True) -> dict
Return analysis diagnostics and summary.
:param data: Result returned by analyze. :param keep: Keep diagnostics by default; the CLI passes False. :returns: Independent diagnostics dictionary. :raises ValueError: analyze has not populated diagnostics.
distribution_figure(data: pd.DataFrame)
Plot qual values without writing files.
:param data: Result table containing qual. :returns: Matplotlib Figure. :raises ValueError: The value column is absent or table is empty.
<!-- api:end -->Show full SKILL.md (177 more words)Show less
Methods and parameters
analyze returns a new DataFrame and leaves the input unchanged.
run_info(result) returns the summary and method diagnostics.
The CLI passes keep=False so diagnostics do not enter output tables.
All calculations are deterministic; synthetic CLI demos retain seed 42.
Gotchas
analyzefilters INFO/DP, not per-sample FORMAT/DP. Missing INFO/DP is treated as zero; each ALT becomes one row.read_recordspreserves VCF header lines in attrs["vcf_headers"]. The legacy CLI filtered.vcf retains DP only and replaces sample genotypes with missing values; do not use it for genotype-preserving filtering.analyzeraises ValueError when no records pass filters, instead of the old CLI failing later with a missing summary key.
Inputs and outputs
Input files:
- File types:
.vcf - VCF structure:
##fileformat; columns:#CHROM,POS,ID,REF,ALT,QUAL,FILTER,INFO
CLI output files:
tables/variants.csvfiltered.vcfreport.mdresult.json- Produces artifact
genomics.filtered_variantsasfiltered.vcf(vcf)
The library writes no files. Steps use write_output; the CLI owns the
listed artifacts. Public figure functions return matplotlib Figures and
do not add new CLI outputs.
CLI
python skills/genomics/genomics-vcf-operations/genomics_vcf_operations.py --input input_file --output results/
python skills/genomics/genomics-vcf-operations/genomics_vcf_operations.py --demo --output /tmp/genomics_vcf_operations_demoSee also
references/parameters.mdreferences/methodology.mdreferences/output_contract.md
Dependencies
numpy, pandas, matplotlib
© TianGzlab, Apache-2.0. Rendered from Markdown: HTML in the file is shown as text, images as links, and headings moved down two levels. Raw file
Files
SKILL.md and 8 other files (references) in skills/genomics/genomics-vcf-operations of TianGzlab/OmicsClaw.
- SKILL.md
- _api.py
- data/example.vcf
- examples/example_step.py
- genomics_vcf_operations.py
- references/methodology.md
- references/output_contract.md
- references/parameters.md
- tests/test_api.py
Open the folder on GitHubat commit 90a3bec
Compare with similar skills
Genomics Vcf Operations 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.
| Skill | Stars | Used in | Tokens | Auto-check | Licence | Repo updated |
|---|---|---|---|---|---|---|
| Genomics Vcf Operations this skillTianGzlab/OmicsClaw | 161 | — | ~1.1k | Automated safety check: Pass | Apache-2.0 | |
| Alphagenome Single Variant Analysisgoogle-deepmind/science-skills | 3.2k | 2 repos | ~3k | Automated safety check: Notes | Apache-2.0 | |
| 13C Metabolic Flux AnalysisK-Dense-AI/scientific-agent-skills | 48k | 1 repos | ~3.2k | Automated safety check: Pass | MIT | |
| Clinvar Databasegoogle-deepmind/science-skills | 3.2k | 2 repos | ~3.9k | Automated safety check: Notes | Apache-2.0 | |
| Metabolic Study Planneraiming-lab/AutoResearchClaw | 15k | — | ~1.9k | Automated safety check: Pass | MIT | |
| Dbsnp Databasegoogle-deepmind/science-skills | 3.2k | 2 repos | ~3.4k | Automated safety check: Notes | Apache-2.0 |
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A skill your agent uses when needing clinical significance, pathogenicity classifications (e.g., Pathogenic, Benign, VUS), clinical evidence rationales, or finding "hard positive" benchmark controls…
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Dbsnp Database
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Runs a metabolic flux analysis from model loading to phenotype prediction and figures by handing work to four sub-agents in sequence.
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Related
Categories
Questions about Genomics Vcf Operations
What does Genomics Vcf Operations do?
Load when summarising / filtering a VCF — variant classification (SNP / MNP / INS / DEL / COMPLEX), Ti/Tv ratio, QUAL / DP threshold filtering, INFO-field parsing. Genomics Vcf Operations is an agent skill from TianGzlab/OmicsClaw. Load when summarising / filtering a VCF — variant classification (SNP / MNP / INS / DEL / COMPLEX), Ti/Tv ratio, QUAL / DP threshold filtering, INFO-field parsing.
When should I use Genomics Vcf Operations?
Genomics Vcf Operations fits situations like: tasks that involve Bioinformatics.
How do I install Genomics Vcf Operations in Claude Code?
Run `npx skills add TianGzlab/OmicsClaw --skill genomics-vcf-operations -a claude-code`. Or copy the skill folder (skills/genomics/genomics-vcf-operations in TianGzlab/OmicsClaw) into .claude/skills/genomics-vcf-operations in your project. Claude Code loads it when a task matches its description.
How do I install Genomics Vcf Operations in Codex?
Run `npx skills add TianGzlab/OmicsClaw --skill genomics-vcf-operations -a codex`. Or copy the skill folder (skills/genomics/genomics-vcf-operations in TianGzlab/OmicsClaw) into .agents/skills/genomics-vcf-operations in your project. Codex loads it when a task matches its description.
Can I use Genomics Vcf Operations 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 TianGzlab/OmicsClaw --skill genomics-vcf-operations -a cursor` (or -a gemini-cli, github-copilot or opencode for the others). To copy it by hand, put the folder in .cursor/skills/genomics-vcf-operations, .gemini/skills/genomics-vcf-operations, .github/skills/genomics-vcf-operations and .opencode/skills/genomics-vcf-operations in your project.
What does Genomics Vcf Operations need to run?
Going by SKILL.md and its folder, Genomics Vcf Operations needs Python for the scripts in its folder and the command-line tools its instructions call (python). Our summary lists: Python 3.
Does Genomics Vcf Operations 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 Genomics Vcf Operations 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 Genomics Vcf Operations use?
Genomics Vcf Operations 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 Genomics Vcf Operations use?
About 1.1k tokens (SKILL.md is roughly 4.5k characters). Agents keep only the skill's name and description in context until a task matches; then they load SKILL.md in full. Its references folder adds about 472 tokens, read only when the agent opens those files.
What are the alternatives to Genomics Vcf Operations?
Skills that share tags, products or a category with Genomics Vcf Operations: Alphagenome Single Variant Analysis (google-deepmind/science-skills, 3.2k stars), 13C Metabolic Flux Analysis (K-Dense-AI/scientific-agent-skills, 48k stars), Clinvar Database (google-deepmind/science-skills, 3.2k stars) and Metabolic Study Planner (aiming-lab/AutoResearchClaw, 15k stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.
Who maintains Genomics Vcf Operations?
TianGzlab (a GitHub organization) maintains it in TianGzlab/OmicsClaw, which has 161 GitHub stars. The repository holds 88 skills in this directory. The repository was last updated on October 7, 2026.
Source: TianGzlab/OmicsClaw on GitHub. Facts on this page come from the repository at the commit we read; the author's words are quoted as theirs.