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Agent skill

Ancestry

by exon-research in exon-research/genomi

Use local ancestry reference-panel tools for 1000 Genomes GRCh37/GRCh38 PCA projection, marker overlap QC, and qualitative reference-neighbor context.

Apache-2.0Auto-check passedResearch & Science

Install Ancestry

skills CLI
$ npx skills add exon-research/genomi --skill ancestry -a claude-code

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

GitHub CLI
$ gh skill install exon-research/genomi ancestry --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/exon-research/genomi.git skills-src && mkdir -p .claude/skills && cp -r skills-src/skills/ancestry .claude/skills/ancestry && 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/

Facts

Skill name
ancestry
GitHub stars
484
Token cost
~2.3k tokens
SKILL.md length
1,078 words
Files
1
Skills in repo
20
Repo updated
First seen
Licence
Apache-2.0

At a glance

Use local ancestry reference-panel tools for 1000 Genomes GRCh37/GRCh38 PCA projection, marker overlap QC, and qualitative reference-neighbor context.

  • Works in 5 steps: Use ancestry.list_reference_panels to… → Use ancestry.build_source_context when… → For sample-specific questions, use… → …
  • Tasks that involve Bioinformatics
  • SKILL.md covers Contract, First Actions, Library Handling and Interpretation Rules, plus 3 more sections
  • Instructions only: no scripts, shell commands, URLs or credentials in SKILL.md

What it does

Ancestry is an agent skill from exon-research/genomi. Use local ancestry reference-panel tools for 1000 Genomes GRCh37/GRCh38 PCA projection, marker overlap QC, and qualitative reference-neighbor context.

Its SKILL.md is about 2.3k tokens, which your agent loads only when the skill is triggered. It is a single SKILL.md file with no bundled scripts.

It sits in Research & Science, covering Bioinformatics. The repository describes itself as: Local-first, open-source Claude Science alternative, before Claude Science is a thing. Turn your AI agent into personal DNA expert. The licence is Apache-2.0.

When your agent uses it

  • Tasks that involve Bioinformatics

Example prompts

  • “/ancestry”

Workflow steps

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

  1. Use ancestry.list_reference_panels to check whether the matching-build
  2. Use ancestry.build_source_context when the user asks what the panel means
  3. For sample-specific questions, use genomi.describe_context only
  4. Use ancestry.estimate_population_context as the default sample-specific
  5. Use ancestry.check_sample_overlap when you only need QC readiness, and

What it can do on your machine

Read from SKILL.md and the folder at commit 1df4f5b. 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

    No scripts in the folder and no shell commands in SKILL.md (its code samples are bash).

    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

Ancestry loads about 2.3k tokens when it runs. Until then it costs about 40 tokens; SKILL.md has 1,078 words of instructions outside code blocks.

Always · name and description, kept in context so the agent knows when to use it
~40
When it runs · the whole SKILL.md, loaded when a task matches
~2.3k

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 exon-research/genomi at commit 1df4f5b, republished under its Apache-2.0 licence (© exon-research). 1,078 words, ~2,255 tokens.

Download SKILL.mdSave it as .claude/skills/ancestry/SKILL.md (or your agent's skills folder).
name
ancestry
description
Use local ancestry reference-panel tools for 1000 Genomes GRCh37/GRCh38 PCA projection, marker overlap QC, and qualitative reference-neighbor context.
tools
genomi.check_libraries, genomi.describe_context, ancestry.list_reference_panels, ancestry.build_source_context, ancestry.check_sample_overlap…
mutating
true

Ancestry Reference-Panel Context

Use this skill when the user asks about ancestry, population context, PCA projection, reference-panel similarity, or which public reference samples their genome is closest to.

Contract

  • This capability is a local reference-panel workflow, not an ethnicity or race predictor.
  • Private tools require current-session Active Genome Index access approval or a genome source path supplied in the current chat.
  • Public metadata tools do not read an Active Genome Index.
  • Private genotype data stays local. Do not upload sample genotypes to external APIs or URLs.
  • The MVP supports GRCh38 and GRCh37. If genome_build is omitted, the tool default is GRCh38 unless an approved Active Genome Index provides another build; the returned defaults_applied records that default.
  • Labels are 1000 Genomes reference-panel labels, not ethnicity, nationality, race, tribe, caste, religion, or personal identity.
  • Output is qualitative reference-panel similarity in PCA space. Do not produce component percentages, admixture proportions, haplogroups, local ancestry, ancestry dates, or relative matching.

Convention: See skills/conventions/context-routing.md. Convention: See skills/conventions/evidence-quality.md. Convention: See skills/_output-rules.md.

First Actions

  1. Use ancestry.list_reference_panels to check whether the matching-build 1000 Genomes 30x panel is installed and to inspect source URLs and label definitions.
  2. Use ancestry.build_source_context when the user asks what the panel means or when you need explicit label and method boundaries before answering.
  3. For sample-specific questions, use genomi.describe_context only when the chat asks about current Active Genome Index context or already mentioned a genome source. If the user supplied a genome source path, that is approval to read it for this session.
  4. Use ancestry.estimate_population_context as the default sample-specific entry point. It runs overlap QC and PCA projection when enough markers are usable.
  5. Use ancestry.check_sample_overlap when you only need QC readiness, and ancestry.project_pca when the host agent needs raw PCA coordinates and nearest reference-neighbor distances.

Library Handling

The required optional library is build-specific: ancestry-1000g-30x-grch38 for GRCh38 samples and ancestry-1000g-30x-grch37 for GRCh37 samples. If a private ancestry tool returns requires_library_install, explain that the compact local panel is needed for marker overlap and PCA projection, then ask before installing with the returned ask_user.install_command or missing_library.install_command. For example:

bash
genomi install --libraries ancestry-1000g-30x-grch38
genomi install --libraries ancestry-1000g-30x-grch38,liftover-chains,ancestry-1000g-30x-grch37

Do not treat a missing panel as evidence about the sample.

Interpretation Rules

  • Report marker overlap, projection readiness, marker-overlap quality, nearest reference group labels, and the method boundary.
  • Marker-overlap quality is graded by the fraction of the loaded panel covered by usable sample dosages. There is no absolute marker-count floor.
  • If less than 20% of the loaded panel is usable, do not project.
  • If 20%-49% of the loaded panel is usable, projection is allowed with low marker-overlap quality and reference-neighbor context only.
  • If 50%-79% of the loaded panel is usable, projection is allowed with moderate marker-overlap quality.
  • If at least 80% of the loaded panel is usable, projection is allowed with high marker-overlap quality.
  • Use wording like: "The sample projects closest to the EUR reference cluster in this panel."
  • Do not say "predict ethnicity", "determine origin", or imply personal identity from a reference-panel label.

User-Facing Answer Shape

If an Active Genome Index was projected, give the qualitative reference-panel similarity, marker-overlap quality, and limitations. If the tool only returned public metadata, answer directly without an Active Genome Index status disclaimer.

Cross-Capability Synthesis

A scope-limited result from this capability is not a final user-facing answer when other Genomi capabilities can contribute orthogonal evidence to the same question. Returning "cannot answer" while applicable capabilities remain unexamined is a host-agent failure mode.

Tools

ancestry.build_source_context

Explain 1000 Genomes ancestry panel provenance, label meanings, sampling limits, and method boundaries.

Use when: The user asks what the ancestry panel means, where labels come from, or why output is reference similarity rather than identity.

Why necessary: Ancestry language is easy to overstate; source context gives agents explicit label and method boundaries before answering.

Not for: Reading or projecting a user's genome; use ancestry.estimate_population_context after approval.

Example prompts: Explain the source and limitations of the ancestry panel.

Result semantics: Public metadata only; no Active Genome Index is read.

Show full SKILL.md (425 more words)Show less
ancestry.check_sample_overlap

Check how many installed 1000 Genomes ancestry panel markers are usable in an approved Active Genome Index.

Use when: The agent needs to know if a selected sample has enough overlap with the installed ancestry reference panel before projection.

Why necessary: Projection is not interpretable below the overlap thresholds; this tool separates QC from interpretation.

Not for: Public panel metadata; use ancestry.list_reference_panels. Ethnicity or origin prediction; ancestry tools provide reference-panel similarity only.

Example prompts: Does my Active Genome Index have enough overlap with the ancestry panel?

Result semantics: Reports usable marker count and projection readiness. It must not be interpreted as ethnicity, nationality, race, tribe, caste, religion, or identity.

ancestry.estimate_population_context

Estimate qualitative reference-panel similarity for an approved GRCh37 or GRCh38 sample using local 1000 Genomes PCA projection.

Use when: The user asks for ancestry or population context from their genome and has approved Active Genome Index use in this session.

Why necessary: Provides a bounded default entry that combines overlap QC and PCA projection while preserving reference-similarity language.

Not for: Ethnicity prediction, determining origin, component percentages, haplogroups, local ancestry, or relative matching.

Example prompts: What 1000 Genomes reference cluster is my Active Genome Index closest to?

Result semantics: The interpretation is qualitative reference-panel similarity only and must never be phrased as ethnicity, nationality, race, tribe, caste, religion, or personal identity.

ancestry.list_reference_panels

List local ancestry reference panels, installation state, public source URLs, label definitions, and method boundaries.

Use when: The user asks what ancestry reference panels are available, whether the 1000 Genomes panel is installed, or what source data and labels are used.

Why necessary: Public panel metadata can be inspected without Active Genome Index access approval and tells agents whether private projection tools are answerable.

Not for: Projecting or interpreting a user's genome; use ancestry.estimate_population_context after Active Genome Index access approval.

Example prompts: What ancestry reference panel does Genomi have installed?

Result semantics: Returns public reference-panel metadata and install status only; it does not read Active Genome Index.

ancestry.project_pca

Project an approved sample into the installed 1000 Genomes ancestry PCA space and return nearest reference neighbors.

Use when: The user or host agent needs PCA coordinates and nearest reference neighbors after scoped Active Genome Index access is approved.

Why necessary: This is the focused computational step behind ancestry.estimate_population_context and avoids component/admixture proportion claims.

Not for: Haplogroups, local ancestry, relative matching, component proportions, or identity/origin prediction.

Example prompts: Project my genome into the matching-build 1000 Genomes PCA panel.

Result semantics: Returns PCA coordinates and reference-neighbor distances only; labels are reference-panel labels, not personal identity labels.

© exon-research, 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

Just SKILL.md in skills/ancestry of exon-research/genomi.

Open the folder on GitHubat commit 1df4f5b

Compare with similar skills

Ancestry 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.

Ancestry compared with similar skills
SkillStarsUsed inTokensAuto-checkLicenceRepo updated
Ancestry this skillexon-research/genomi484—~2.3kAutomated safety check: PassApache-2.0
Alphagenome Single Variant Analysisgoogle-deepmind/science-skills3.2k2 repos~3kAutomated safety check: NotesApache-2.0
13C Metabolic Flux AnalysisK-Dense-AI/scientific-agent-skills48k1 repos~3.2kAutomated safety check: PassMIT
Clinvar Databasegoogle-deepmind/science-skills3.2k2 repos~3.9kAutomated safety check: NotesApache-2.0
Metabolic Study Planneraiming-lab/AutoResearchClaw15k—~1.9kAutomated safety check: PassMIT
Dbsnp Databasegoogle-deepmind/science-skills3.2k2 repos~3.4kAutomated safety check: NotesApache-2.0

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More from exon-research/genomi

All 20 skills in this repo

  • Genomi

    exon-research/genomi

    A skill your agent uses for genetics, genome source, variant, gene, phenotype, disease, screen, pharmacogenomics, and Genomi install/setup maintenance questions.

    484 GitHub stars~4k tokensUpdated 1 mo ago
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  • Genomi Gnomad

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    Fetch reusable public population allele frequencies from gnomAD for a specific variant.

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  • Genomilab

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    Run or continue patient-authorized, genome-informed GenomiLab investigations in the current Claude, Codex, or other MCP agent task.

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  • Analytical Grounding

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    484 GitHub stars~1.2k tokensUpdated 1 mo ago
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  • Clinvar

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  • Active Genome Index

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Categories

Questions about Ancestry

What does Ancestry do?

Use local ancestry reference-panel tools for 1000 Genomes GRCh37/GRCh38 PCA projection, marker overlap QC, and qualitative reference-neighbor context. Ancestry is an agent skill from exon-research/genomi. Use local ancestry reference-panel tools for 1000 Genomes GRCh37/GRCh38 PCA projection, marker overlap QC, and qualitative reference-neighbor context.

When should I use Ancestry?

Ancestry fits situations like: tasks that involve Bioinformatics.

How do I install Ancestry in Claude Code?

Run `npx skills add exon-research/genomi --skill ancestry -a claude-code`. Or copy the skill folder (skills/ancestry in exon-research/genomi) into .claude/skills/ancestry in your project. Claude Code loads it when a task matches its description.

How do I install Ancestry in Codex?

Run `npx skills add exon-research/genomi --skill ancestry -a codex`. Or copy the skill folder (skills/ancestry in exon-research/genomi) into .agents/skills/ancestry in your project. Codex loads it when a task matches its description.

Can I use Ancestry 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 exon-research/genomi --skill ancestry -a cursor` (or -a gemini-cli, github-copilot or opencode for the others). To copy it by hand, put the folder in .cursor/skills/ancestry, .gemini/skills/ancestry, .github/skills/ancestry and .opencode/skills/ancestry in your project.

What does Ancestry need to run?

SKILL.md names no scripts, command-line tools or credentials: Ancestry is instructions for the agent only.

Does Ancestry 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 Ancestry 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 Ancestry use?

Ancestry 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 Ancestry use?

About 2.3k tokens (SKILL.md is roughly 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 Ancestry?

Skills that share tags, products or a category with Ancestry: 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 Ancestry?

exon-research (a GitHub organization) maintains it in exon-research/genomi, which has 484 GitHub stars. The repository holds 20 skills in this directory. The repository was last updated on August 31, 2026.

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