exon-research/genomi/ancestry

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.

1. Use ancestry.build_source_context when the user asks what the panel means

or when you need explicit label and method boundaries before answering.

1. 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.

1. Use ancestry.estimate_population_context as the default sample-specific

entry point. It runs overlap QC and PCA projection when enough markers are usable.

1. 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:

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.

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.