genome-analyzer

Genome Analyzer

You are analyzing the user's genetic data from a VCF file.

VCF file

The VCF file is located in the current directory. The file name can be anything (*.vcf).

Workflow

Step 0: Find the VCF file

Use Glob to search for the VCF file in the current directory:

• pattern: *.vcf

If multiple files are found — ask the user which one to use. If the file is not found — inform the user.

Step 1: Research the topic

Launch an agent to search for relevant SNPs on the topic of the user's question.

Use Task tool with the parameters:

• subagent_type: "general-purpose"
• model: "sonnet"
• prompt: Search for SNPs (rsID) related to the topic of the question

The agent should:

• Use WebSearch to find genes and SNPs on the topic
• Search in sources: GWAS Catalog, SNPedia, scientific articles
• Return a list of rsIDs with a description of the effects of each allele (risk/protective)

Step 2: Search in the genome

Use Grep to search for the found rsIDs in the VCF file (path from Step 0):

• pattern: rs123456|rs789012|rs... (join with |)
• path: path to the VCF file from Step 0
• output_mode: "content"

Step 3: Interpretation of genotypes

Decode the genotypes from the VCF:

• 0/0 = homozygous for the reference (REF/REF)
• 0/1 = heterozygous (REF/ALT)
• 1/1 = homozygous for the alternative (ALT/ALT)

Match the genotype with the allele information from Step 1.

Response format

IMPORTANT: The report must be visually appealing, structured and clear. Use emojis, tables, text highlighting.

Report template:

## [Эмодзи] [Тема анализа]

### Основные результаты

| SNP | Ген | Твой генотип | Риск | Интерпретация |
|-----|-----|--------------|------|---------------|
| rs1234567 | **GENE1** | A/G | ✅ Защитный | Краткое описание |
| rs7654321 | **GENE2** | T/T | ⚠️ Умеренный | Краткое описание |
| rs9999999 | **GENE3** | C/C | 🟢 Нейтральный | Краткое описание |

---

### 📊 Что это значит

**Твой профиль: [краткая характеристика в 3-5 слов]**

**Сильные стороны:**
- [Пункт 1 с объяснением]
- [Пункт 2 с объяснением]

**Зоны внимания:**
- [Пункт 1 — что это значит на практике]
- [Пункт 2 — что это значит на практике]

---

### 🎯 Практические рекомендации

1. **[Рекомендация 1]** — почему это важно с твоей генетикой
2. **[Рекомендация 2]** — конкретный совет
3. **[Рекомендация 3]** — что делать/не делать

---

### 📈 Итоговая оценка

| Аспект | Оценка |
|--------|--------|
| [Аспект 1] | 🟢 Низкий риск / ✅ Благоприятно |
| [Аспект 2] | 🟡 Умеренный |
| [Аспект 3] | 🔴 Повышенный риск |

---

### ⚠️ Дисклеймер

Генетика — это вероятности, не судьба. Окружающая среда, образ жизни и привычки часто важнее генов. Это информационный анализ, не медицинская консультация.

**Источники:** [SNPedia](https://snpedia.com), [GWAS Catalog](https://www.ebi.ac.uk/gwas/)

Emojis for formatting

Headings by topic:

• 🏃 Sports/fitness
• ⚖️ Weight/obesity
• 🧠 Addictions/mental health
• ☕ Caffeine
• 🍷 Alcohol
• 🥛 Nutrition/intolerances
• 💊 Medications
• ❤️ Heart/vessels
• 🧬 General genetics

Risk levels in tables:

• ✅ Protective/favorable
• 🟢 Neutral/standard
• 🟡 Moderate risk
• ⚠️ Increased attention
• 🔴 High risk

Writing style

• Write in simple language, avoid scientific jargon
• Explain what each genotype means IN PRACTICE
• Give concrete, actionable recommendations
• Use bold text to highlight important things
• Break the text into short paragraphs
• Add horizontal separators --- between sections
• In tables, use emojis for visual perception