genomic-inquiry

Genomic Inquiry

Use this skill as the default entry for natural-language DNA questions: personal triage, "what matters in my genome?", "do I have this variant?", variant/gene interpretation, GWAS-style questions, or public genomic background.

Goal

Turn the user's question into the smallest useful evidence action. A genome source is optional context. Use the Active Genome Index when present and relevant; with public-only context, answer from public sources, GWAS, and shared reviewed evidence.

Convention: See skills/conventions/context-routing.md before selecting Active Genome Index. Convention: See skills/conventions/evidence-quality.md before making personal or medical claims.

Contract

Contract:

• User intent drives the selected evidence path.
• The host agent resolves intent from this skill pack and tool outputs.
• Personal claims use only explicitly selected session context.
• Public-source answers do not need a routine Active Genome Index status line.
• Tool outputs are inspected before choosing additional operations.
• Operation metadata and focused skills guide tool choice; tool results are evidence for the host agent to interpret.
• Candidate and ranking tools return evidence views, alternatives, warnings, coverage, and source-prior detail for the host agent to interpret.

Agent Start

1. Use genomi.describe_context when the Active Genome Index is unknown.
2. Extract obvious fields from the user request: source, agi_id, user/profile nickname, rsid, gene, exact allele, phenotype, drug, condition, or topic.
3. Load the most specific focused capability skill, then call its capability tools through genomi.invoke.
4. Call one narrow tool and inspect its output before selecting additional evidence operations.

Personal Source Triage

For "what matters in my genome?" or similar broad personal questions:

• If a source path is supplied, build/select it with genomi.parse_source when an Active Genome Index is needed. The supplied source path is approval to read that source for this session.
• Run clinvar.scan_candidates to build a deterministic ClinVar candidate inventory. If the build-specific ClinVar library is missing, ask before installing clinvar-grch38 or clinvar-grch37.
• Inspect structured candidate guidance before selecting findings for follow-up or final interpretation.
• Drill into selected findings with variant.gather_allele_context, variant.gather_gene_context, active_genome_index.classify_genotype_support, or active_genome_index.classify_region_callability.