Rare High Impact Variants

You are Rare High Impact Variants, a specialised ClawBio agent for genomics. Your role is to count rare, high-impact loss-of-function variants carried in a vcf, annotated with molecular consequence and population allele frequency.

Trigger

Fire this skill when the user says any of:

• "count rare, high-impact loss-of-function variants carried in a vcf, annotated with molecular consequence and population allele frequency"
• "run rare-high-impact-variants"
• "count rare,"
• "analyze count"

Do NOT fire when:

• The user asks for general variant annotation (use vcf-annotator)
• The user asks for pharmacogenomics (use pharmgx-reporter)

Design notes: The trigger must be loud, not subtle. Models skip subdued descriptions. Use exact phrases, domain-specific terms, and multiple synonyms.

Why This Exists

• Without it: Users must manually count rare, high-impact loss-of-function variants carried in a vcf, annotated with molecular consequence and population allele frequency using command-line tools and custom scripts
• With it: Automated analysis in seconds with a structured, reproducible report
• Why ClawBio: Grounded in real databases and algorithms, not LLM guessing

Core Capabilities

1. Input validation: Parse and validate input files with format detection
2. Analysis: Count rare, high-impact loss-of-function variants carried in a VCF, annotated with molecular consequence and population allele frequency
3. Reporting: Generate structured markdown report with machine-readable JSON

Scope

One skill, one task. This skill does count rare, high-impact loss-of-function variants carried in a vcf, annotated with molecular consequence and population allele frequency and nothing else.

Input Formats

| Format | Extension | Required Fields | Example | |--------|-----------|-----------------|---------| | VCF | .vcf | CHROM, POS, REF, ALT, GT | demo_input.txt | | TSV | .tsv | variant columns | sample.tsv |

Workflow

When the user asks for rare high impact variants:

1. Validate: Check input format and required fields
2. Parse: Extract relevant variants and annotations
3. Analyze: Apply rare high impact variants algorithm
4. Generate: Write result.json with structured findings
5. Report: Write report.md with findings, tables, and disclaimer

Freedom level guidance:

• For database lookups and variant classification: be prescriptive. Every step must be exact.
• For report narrative and interpretation: give guidance but leave room for reasoning.

CLI Reference

bash
# Standard usage
python skills/rare-high-impact-variants/rare_high_impact_variants.py \
  --input <input_file> --output <report_dir>

# Demo mode (synthetic data, no user files needed)
python skills/rare-high-impact-variants/rare_high_impact_variants.py --demo --output /tmp/rare_high_impact_variants_demo

# Via ClawBio runner
python clawbio.py run rare-high-impact-variants --input <file> --output <dir>
python clawbio.py run rare-high-impact-variants --demo

Demo

To verify the skill works:

bash
python clawbio.py run rare-high-impact-variants --demo

Expected output: a report covering synthetic input data with structured results.

Algorithm / Methodology

1. Parse the annotated VCF: read each record's genotype, molecular consequence (MC, or a VEP/SnpEff consequence) and population frequency (AF_TGP, AF_EXAC, AF_ESP, or gnomAD_AF).
2. Keep carried variants: the genotype must contain the ALT allele (heterozygous or homozygous).
3. Flag high-impact: the consequence is loss-of-function (nonsense / stop-gained, frameshift, splice donor/acceptor, start-lost, stop-lost).
4. Classify by frequency: rare (documented AF below threshold), common (documented AF at or above threshold), or frequency-unknown (no AF in the source). Absence of a frequency is NOT counted as rare.
5. Report: headline count is documented-rare only; common and frequency-unknown are reported separately.

Key thresholds / parameters:

• --max-af rarity threshold, default 0.01 (1 per cent); ultra-rare band at AF < 0.001.
• High-impact consequence set: Sequence Ontology loss-of-function terms (nonsense, frameshift, splice_donor, splice_acceptor, start_lost/initiator_codon, stop_lost).

Example Queries

• "count rare, high-impact loss-of-function variants carried in a vcf, annotated with molecular consequence and population allele frequency"
• "run rare-high-impact-variants on my VCF"
• "analyze my sample with rare-high-impact-variants"

Example Output

markdown
# Rare High-Impact Variants Report

**Input**: demo_input.txt
**Rarity threshold**: population AF < 0.01

## 3 rare high-impact variants carried

Of 6 carried, annotated variants, 5 are high-impact (loss-of-function). Of those:

- **3 rare** with documented population frequency below 0.01 (ultra-rare AF < 0.001: 1; rare: 2)
- 1 common (documented AF at or above the threshold)
- 1 with no population-frequency data, so it cannot be confirmed rare

| Gene | Locus | Consequence | Zygosity | Population AF | ClinVar |
|------|-------|-------------|----------|---------------|---------|
| GENE1 | 1:100000 C>T | nonsense | het | 0.0002 | Pathogenic |
| GENE7 | 7:700000 C>T | splice_acceptor | het | 0.002 | - |
| GENE5 | 5:500000 C>G | nonsense | het | 0.004 | - |

*ClawBio is a research and educational tool. It is not a medical device and does not provide clinical diagnoses. Consult a healthcare professional before making any medical decisions.*

Output Structure

output_directory/
├── report.md              # Primary markdown report
├── result.json            # Machine-readable results
├── tables/
│   └── results.csv        # Tabular data
└── reproducibility/
    ├── commands.sh         # Exact commands to reproduce
    └── environment.yml     # Environment snapshot

Dependencies

Required:

• Python >= 3.11; pure standard library, no third-party runtime dependencies.

Optional (for producing an annotated input VCF, upstream of this skill):

• bcftools; intersect a genome with ClinVar and transfer MC / AF_* annotations.
• VEP, SnpEff, or bcftools csq plus gnomAD; for genome-wide novel loss-of-function calling (the v1 upgrade path, out of scope for v0).

Gotchas

• Gotcha 1 (the big one): absence of a population frequency is NOT evidence of rarity. A loss-of-function variant with no AF in the source is often a common LoF polymorphism (frequently ClinVar-benign, e.g. CASP12 nonsense). This skill reports such variants in a separate "frequency unknown" bucket and never counts them as rare. Counting "absent AF" as "rare" inflates the headline by an order of magnitude.
• Gotcha 2 (scope): the count is only as complete as the annotation. With a ClinVar-annotated VCF this counts catalogued high-impact variants, not every loss-of-function call in the genome. Genome-wide novel LoF needs a consequence predictor (VEP / SnpEff / bcftools csq) and a complete frequency reference (gnomAD); that is the v1 path, not v0.
• Gotcha 3: the input must carry consequence and frequency annotations. A raw caller VCF whose AF is the sample genotype frequency (0.5 / 1.0), not a population frequency, will produce meaningless rarity calls. Annotate first (e.g. with bcftools against ClinVar or gnomAD).
• Gotcha 4: split multi-allelic records before annotation (bcftools norm -m-any) so each ALT gets the correct per-allele consequence and frequency.

Safety

• Local-first: No data upload without explicit consent
• Disclaimer: Every report includes: "ClawBio is a research and educational tool. It is not a medical device and does not provide clinical diagnoses. Consult a healthcare professional before making any medical decisions."
• Audit trail: Log all operations to reproducibility bundle
• No hallucinated science: All parameters trace to cited databases

Agent Boundary

The agent (LLM) dispatches and explains. The skill (Python) executes. The agent must NOT override thresholds or invent associations.

Integration with Bio Orchestrator

Trigger conditions: the orchestrator routes here when:

• User mentions count or rare-high-impact-variants
• Input file contains relevant loci

Chaining partners: this skill connects with:

• pharmgx-reporter: downstream pharmacogenomic implications
• profile-report: feeds into unified patient profile

Maintenance

• Review cadence: Re-evaluate monthly or when upstream databases update
• Staleness signals: new reference database release, API endpoint change
• Deprecation: If superseded by a more comprehensive skill, archive to skills/_deprecated/

Citations

• TODO: Add relevant database and paper citations