Menu
Use local ancestry reference-panel tools for 1000 Genomes GRCh37/GRCh38 PCA projection, marker overlap QC, and qualitative reference-neighbor context.
Install with Codex or Claude Copy this prompt, paste it into Codex, Claude, or another assistant, and let it review the skill page and install it for you.
Based on SOC occupation classification
Use this skill for genetics, genome source, variant, gene, phenotype, disease, screen, pharmacogenomics, and Genomi install/setup maintenance questions.
Build and inspect ClinVar exact-match evidence and candidate inventories. Use for clinical labels, VUS/conflict, carrier context, and drug-response rows.
Activate this skill for "/genomi decode", "decode my genome", "decode my DNA", "show me the dashboard", "the Genomi dashboard", "one-shot rundown", or any all-at-once request that asks Genomi to compose every capability's findings into a single artifact. This is the whole-genome dashboard kicker — it sweeps every relevant Genomi capability in one shot, not a per-target lookup. Composes evidence from every relevant Genomi capability into a single self-contained Genomi Dashboard.html and returns localhost serve metadata. Active genome required.
Answer drug-response, medication, PharmGKB-style, PGxDB, ATC, DrugBank, gene-drug, and variant-drug questions using public PGx evidence plus local sample genotype support when an Active Genome Index is selected.
Plan rare disease, hereditary disease, cancer risk, carrier-relevance, and observed-condition source investigation from public targets or selected active genome evidence.
Answer specific rsID, allele, gene, region, genotype, and absence/callability questions using explicit session context or public evidence.
| 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","ancestry.project_pca","ancestry.estimate_population_context","active_genome_index.approve_access","genomi.parse_source"] |
| mutating | true |
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.
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.Convention: See
skills/conventions/context-routing.md. Convention: Seeskills/conventions/evidence-quality.md. Convention: Seeskills/_output-rules.md.
ancestry.list_reference_panels to check whether the matching-build
1000 Genomes 30x panel is installed and to inspect source URLs and label
definitions.ancestry.build_source_context when the user asks what the panel means
or when you need explicit label and method boundaries before answering.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.ancestry.estimate_population_context as the default sample-specific
entry point. It runs overlap QC and PCA projection when enough markers are
usable.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.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.
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.
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.
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.
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.
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.
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.
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.