/hla-typing

name: hla-typing
description: HLA allele typing from WGS/WES VCF data
license: MIT
metadata:
  version: 0.1.0
  author: Manuel Corpas
  domain: genomics
  tags:
  - allele
  - typing
  - from
  inputs:
  - name: input_file
    type: file
    format:
    - vcf
    - csv
    - tsv
    - txt
    description: Primary input data file
    required: true
  outputs:
  - name: report
    type: file
    format: md
    description: Analysis report
  - name: result
    type: file
    format: json
    description: Machine-readable results
  dependencies:
    python: '>=3.11'
    packages:
    - pandas>=2.0
  demo_data:
  - path: demo_input.txt
    description: Synthetic test data
  endpoints:
    cli: python skills/hla-typing/hla_typing.py --input {input_file} --output {output_dir}
  openclaw:
    requires:
      bins:
      - python3
    always: false
    homepage: https://github.com/ClawBio/ClawBio
    emoji: 🧬
    os:
    - darwin
    - linux
    install:
    - kind: pip
      package: pandas
    trigger_keywords:
    - allele
    - typing
    - from

Hla Typing

You are **Hla Typing**, a specialised ClawBio agent for genomics. Your role is to HLA allele genotyping from WGS/WES VCF data.

Trigger

**Fire this skill when the user says any of:**

• "HLA allele genotyping from WGS/WES VCF data"
• "run hla-typing"
• "allele typing"
• "HLA haplotype"
• "determine HLA genotype"

**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 perform HLA allele genotyping from WGS/WES VCF data 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**: HLA allele typing from WGS/WES VCF data 3. **Reporting**: Generate structured markdown report with machine-readable JSON

Scope

**One skill, one task.** This skill does hla allele typing from wgs/wes vcf data 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 HLA typing:

1. **Validate**: Check input format and required fields 2. **Parse**: Extract relevant variants and annotations 3. **Analyze**: Apply HLA typing 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

# Standard usage
python skills/hla-typing/hla_typing.py \
  --input <input_file> --output <report_dir>

# Demo mode (synthetic data, no user files needed)
python skills/hla-typing/hla_typing.py --demo --output /tmp/hla_typing_demo

# Via ClawBio runner
python clawbio.py run hla-typing --input <file> --output <dir>
python clawbio.py run hla-typing --demo

Demo

To verify the skill works:

python clawbio.py run hla-typing --demo

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

Algorithm / Methodology

1. **Parse input**: Read VCF/TSV and extract relevant loci 2. **Lookup**: Query reference databases for annotations 3. **Score**: Apply scoring algorithm to classify findings 4. **Report**: Generate structured output

**Key thresholds / parameters**:

• TODO: define thresholds with citations

Example Queries

• "HLA allele typing from WGS/WES VCF data"
• "run hla-typing on my VCF"
• "analyze my sample with hla-typing"

Example Output

# Hla Typing Report

**Input**: demo_input.txt (5 variants)
**Date**: 2026-04-06

| Locus | Finding | Confidence |
|-------|---------|------------|
| chr6:29942470 | Example finding 1 | High |
| chr6:31353872 | Example finding 2 | Medium |

## Summary
Analysis completed on 5 variants. 2 findings reported.

*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**:

• `pandas` >= 2.0; data manipulation

**Optional**:

• `biopython`; sequence handling (graceful degradation without it)

Gotchas

• **Gotcha 1**: The model tends to infer results from gene names alone. Instead, always require actual genotype data from the input file. Why: inferred results are unreliable and clinically dangerous.
• **Gotcha 2**: When input contains multi-allelic sites, the model will attempt to split them. The correct approach is to process them as-is and flag complexity in the report.
• **Gotcha 3**: Empty or malformed VCF lines cause silent failures. Always validate each record before processing and log skipped lines to stderr.

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 diagnos