Agent skill

Hla Typing

“HLA allele typing from WGS/WES VCF data”

— description from SKILL.md by ClawBio

Install Hla Typing

skills CLI

$ npx skills add ClawBio/ClawBio --skill hla-typing -a claude-code

Project install by default; add -g for ~/.claude/skills/.

GitHub CLI

$ gh skill install ClawBio/ClawBio hla-typing --agent claude-code

Project scope by default; add --scope user for a personal install. Needs GitHub CLI 2.90.0 or later (public preview).

Manual copy

$ git clone --depth 1 https://github.com/ClawBio/ClawBio.git skills-src && mkdir -p .claude/skills && cp -r skills-src/skills/hla-typing .claude/skills/hla-typing && rm -rf skills-src

Use ~/.claude/skills/ instead of .claude/skills for a personal install. The folder must contain SKILL.md.

Claude Code skills documentation · loads skills from .claude/skills/

Paste into Claude Code

Install the "hla-typing" agent skill from https://github.com/ClawBio/ClawBio/tree/main/skills/hla-typing into .claude/skills/hla-typing/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "hla-typing", then confirm the skill loads.

Claude Code copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.

$skill-installer

$skill-installer install https://github.com/ClawBio/ClawBio/tree/main/skills/hla-typing

Type this inside Codex. $skill-installer <name> installs a curated skill from openai/skills. The installer writes to $CODEX_HOME/skills (default ~/.codex/skills). Restart Codex if the skill does not show up.

skills CLI

$ npx skills add ClawBio/ClawBio --skill hla-typing -a codex

Project install goes to .agents/skills/; add -g for ~/.codex/skills/.

GitHub CLI

$ gh skill install ClawBio/ClawBio hla-typing --agent codex

Project scope by default (.agents/skills/); add --scope user for a personal install.

Manual copy

$ git clone --depth 1 https://github.com/ClawBio/ClawBio.git skills-src && mkdir -p .agents/skills && cp -r skills-src/skills/hla-typing .agents/skills/hla-typing && rm -rf skills-src

Use ~/.agents/skills/ instead of .agents/skills for a personal install.

Codex skills documentation · loads skills from .agents/skills/

Paste into Codex

Install the "hla-typing" agent skill from https://github.com/ClawBio/ClawBio/tree/main/skills/hla-typing into .agents/skills/hla-typing/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "hla-typing", then confirm the skill loads.

Codex copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.

skills CLI

$ npx skills add ClawBio/ClawBio --skill hla-typing -a cursor

Project install goes to .agents/skills/; add -g for ~/.cursor/skills/.

GitHub CLI

$ gh skill install ClawBio/ClawBio hla-typing --agent cursor

Project scope by default (.agents/skills/); add --scope user for a personal install.

Manual copy

$ git clone --depth 1 https://github.com/ClawBio/ClawBio.git skills-src && mkdir -p .cursor/skills && cp -r skills-src/skills/hla-typing .cursor/skills/hla-typing && rm -rf skills-src

Use ~/.cursor/skills/ instead of .cursor/skills for a personal install.

Cursor skills documentation · loads skills from .cursor/skills/, .agents/skills/, .claude/skills/, .codex/skills/

Paste into Cursor

Install the "hla-typing" agent skill from https://github.com/ClawBio/ClawBio/tree/main/skills/hla-typing into .cursor/skills/hla-typing/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "hla-typing", then confirm the skill loads.

Cursor copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.

gemini skills install

$ gemini skills install https://github.com/ClawBio/ClawBio.git --path skills/hla-typing

--scope user (default) or --scope workspace; --path is the subfolder of the repo that holds the skill; --consent skips the security confirmation prompt.

skills CLI

$ npx skills add ClawBio/ClawBio --skill hla-typing -a gemini-cli

Project install goes to .agents/skills/; add -g for ~/.gemini/skills/.

GitHub CLI

$ gh skill install ClawBio/ClawBio hla-typing --agent gemini-cli

Project scope by default (.agents/skills/); add --scope user for a personal install.

Manual copy

$ git clone --depth 1 https://github.com/ClawBio/ClawBio.git skills-src && mkdir -p .gemini/skills && cp -r skills-src/skills/hla-typing .gemini/skills/hla-typing && rm -rf skills-src

Use ~/.gemini/skills/ instead of .gemini/skills for a personal install, then run /skills reload.

Gemini CLI skills documentation · loads skills from .gemini/skills/, .agents/skills/

Paste into Gemini CLI

Install the "hla-typing" agent skill from https://github.com/ClawBio/ClawBio/tree/main/skills/hla-typing into .gemini/skills/hla-typing/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "hla-typing", then confirm the skill loads.

Gemini CLI copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.

GitHub CLI

$ gh skill install ClawBio/ClawBio hla-typing

Installs for Copilot at project scope by default; add --scope user for a personal install. Preview a skill first with gh skill preview. Needs GitHub CLI 2.90.0 or later (public preview).

skills CLI

$ npx skills add ClawBio/ClawBio --skill hla-typing -a github-copilot

Project install goes to .agents/skills/; add -g for ~/.copilot/skills/.

Manual copy

$ git clone --depth 1 https://github.com/ClawBio/ClawBio.git skills-src && mkdir -p .github/skills && cp -r skills-src/skills/hla-typing .github/skills/hla-typing && rm -rf skills-src

Use ~/.copilot/skills/ instead of .github/skills for a personal install. Commit .github/skills so cloud agent and code review can use it.

GitHub Copilot skills documentation · loads skills from .github/skills/, .claude/skills/, .agents/skills/

Paste into GitHub Copilot

Install the "hla-typing" agent skill from https://github.com/ClawBio/ClawBio/tree/main/skills/hla-typing into .github/skills/hla-typing/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "hla-typing", then confirm the skill loads.

GitHub Copilot copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.

skills CLI

$ npx skills add ClawBio/ClawBio --skill hla-typing -a opencode

OpenCode documents no install command of its own. Project install goes to .agents/skills/; add -g for ~/.config/opencode/skills/.

GitHub CLI

$ gh skill install ClawBio/ClawBio hla-typing --agent opencode

Project scope by default (.agents/skills/); add --scope user for a personal install.

Manual copy

$ git clone --depth 1 https://github.com/ClawBio/ClawBio.git skills-src && mkdir -p .opencode/skills && cp -r skills-src/skills/hla-typing .opencode/skills/hla-typing && rm -rf skills-src

Use ~/.config/opencode/skills/ instead of .opencode/skills for a personal install.

OpenCode skills documentation · loads skills from .opencode/skills/, .claude/skills/, .agents/skills/

Paste into OpenCode

Install the "hla-typing" agent skill from https://github.com/ClawBio/ClawBio/tree/main/skills/hla-typing into .opencode/skills/hla-typing/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "hla-typing", then confirm the skill loads.

OpenCode copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.

Facts

Skill name: hla-typing
GitHub stars: 1.2k
Used in: 1 other repo
Token cost: ~1.8k tokens
SKILL.md length: 605 words
Files: 11
Skills in repo: 104
Repo updated: Oct 7, 2026
First seen: Oct 7, 2026
Licence: MIT

At a glance

Works in 3 steps: Input validation: Parse and validate… → Analysis: HLA allele typing from WGS/WES… → Reporting: Generate structured markdown…
SKILL.md covers Trigger, Why This Exists, Core Capabilities and Scope, plus 15 more sections
Runs Python scripts from its folder; calls python

About this skill

Hla Typing is a skill in ClawBio/ClawBio (1.2k stars). Its SKILL.md is about 1.8k tokens, with 10 other files in the folder, and copies of it appear in 1 other owners' repositories. Licence: MIT.

Workflow steps

3 steps, taken from the first numbered list in SKILL.md.

Input validation: Parse and validate input files with format detection
Analysis: HLA allele typing from WGS/WES VCF data
Reporting: Generate structured markdown report with machine-readable JSON

What it can do on your machine

Read from SKILL.md and the folder at commit 5e045e3. It shows what the files ask for, not the result of running them.

Tool permissions
Pre-approves nothing: there is no allowed-tools line, so your agent's usual permission prompts apply.
From allowed-tools in the SKILL.md frontmatter.
Runs code
Ships script files (Python), which the agent can run.
Shell commands in SKILL.md call:
- python
From the folder's file list and the shell code blocks in SKILL.md.
Network
No URLs in SKILL.md.
From URLs in SKILL.md, links to its own repository left out.
Credentials
Names no API keys, tokens, secrets or passwords.
From names ending in _API_KEY, _TOKEN, _SECRET, _KEY or _PASSWORD in SKILL.md.

Context cost

Hla Typing loads about 1.8k tokens when it runs. Until then it costs about 13 tokens; SKILL.md has 605 words of instructions outside code blocks.

Always · name and description, kept in context so the agent knows when to use it: ~13
When it runs · the whole SKILL.md, loaded when a task matches: ~1.8k

Estimates: characters ÷ 4, the usual rule of thumb; real counts depend on the model's tokenizer. Scripts and assets cost tokens only if the agent reads them.

Safety

Auto-check passed

The automated check found no risky patterns in SKILL.md.

Automated static check — not a guarantee. Review scripts before installing. It scans the text of SKILL.md for risky patterns (piping downloads into a shell, reading credential files, hidden Unicode, destructive commands); files beside SKILL.md are not scanned.

SKILL.md

The full file from ClawBio/ClawBio at commit 5e045e3, republished under its MIT licence (© ClawBio). 605 words, ~1,759 tokens.

Download SKILL.mdSave it as .claude/skills/hla-typing/SKILL.md (or your agent's skills folder). This skill also uses 10 other files; get the full folder from GitHub.

name: hla-typing
description: HLA allele typing from WGS/WES VCF data
license: MIT
metadata.version: 0.1.0
metadata.author: Manuel Corpas
metadata.domain: genomics
metadata.tags: 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

Input validation: Parse and validate input files with format detection
Analysis: HLA allele typing from WGS/WES VCF data
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:

Validate: Check input format and required fields
Parse: Extract relevant variants and annotations
Analyze: Apply HLA typing algorithm
Generate: Write result.json with structured findings
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/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:

bash

python clawbio.py run hla-typing --demo

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

Algorithm / Methodology

Parse input: Read VCF/TSV and extract relevant loci
Lookup: Query reference databases for annotations
Score: Apply scoring algorithm to classify findings
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

markdown

# 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

Show full SKILL.md (248 more words)Show less

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 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 allele or hla-typing
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

Files

SKILL.md and 10 other files in skills/hla-typing of ClawBio/ClawBio.

SKILL.md
api.py
bench_test_cases/ht_01_basic_correct/ground_truth.txt
bench_test_cases/ht_01_basic_correct/input.txt
bench_test_cases/ht_02_empty_input/ground_truth.txt
bench_test_cases/ht_02_empty_input/input.txt
bench_test_cases/ht_03_malformed_input/ground_truth.txt
bench_test_cases/ht_03_malformed_input/input.txt
demo_input.txt
hla_typing.py
tests/test_hla_typing.py

Open the folder on GitHubat commit 5e045e3

Used in 1 other repository

We found 1 copy of this SKILL.md (exact, near-identical or edited) in other folders, from 1 other GitHub owner. This page covers the copy in ClawBio/ClawBio, which our catalogue first saw on October 7, 2026.

majiayu000/claude-skill-registryskills/bash/hla-typing

Compare with similar skills

Hla Typing next to the 5 skills that share the most tags, products or categories with it. Stars are the repository's; “used in” counts other GitHub owners with a copy.

Hla Typing compared with similar skills
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Content Research Writerweapp-tailwindcss/weapp-tailwindcss	1.9k	25 repos	~3.5k	Automated safety check: Pass	MIT	today

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Questions about Hla Typing

How do I install Hla Typing in Claude Code?

Run `npx skills add ClawBio/ClawBio --skill hla-typing -a claude-code`. Or copy the skill folder (skills/hla-typing in ClawBio/ClawBio) into .claude/skills/hla-typing in your project. Claude Code loads it when a task matches its description.

How do I install Hla Typing in Codex?

Run `npx skills add ClawBio/ClawBio --skill hla-typing -a codex`. Or copy the skill folder (skills/hla-typing in ClawBio/ClawBio) into .agents/skills/hla-typing in your project. Codex loads it when a task matches its description.

Can I use Hla Typing in Cursor, Gemini CLI or GitHub Copilot?

Cursor, Gemini CLI, GitHub Copilot and OpenCode also load SKILL.md folders. With the skills CLI, run `npx skills add ClawBio/ClawBio --skill hla-typing -a cursor` (or -a gemini-cli, github-copilot or opencode for the others). To copy it by hand, put the folder in .cursor/skills/hla-typing, .gemini/skills/hla-typing, .github/skills/hla-typing and .opencode/skills/hla-typing in your project.

What does Hla Typing need to run?

Going by SKILL.md and its folder, Hla Typing needs Python for the scripts in its folder and the command-line tools its instructions call (python).

Does Hla Typing access the network?

SKILL.md contains no URLs. Any network use would come from the scripts or tools the agent runs. This is read from the text; nothing was executed.

Is Hla Typing safe to install?

Our automated static check of SKILL.md found no risky patterns, such as piping downloads into a shell, reading credential files or hidden Unicode. It is not a guarantee. Review the folder before installing.

What licence does Hla Typing use?

Hla Typing is published under the MIT licence (declared in SKILL.md). It allows redistribution, so the full SKILL.md is shown on this page.

How many tokens does Hla Typing use?

About 1.8k tokens (SKILL.md is roughly 7k characters). Agents keep only the skill's name and description in context until a task matches; then they load SKILL.md in full.

What are the alternatives to Hla Typing?

Skills that share tags, products or a category with Hla Typing: Hypothesis Generation (spacering-net/codeg, 3.8k stars), GitHub Deep Research (bytedance/deer-flow, 83k stars), Nature Paper Card (Yuan1z0825/nature-skills, 46k stars) and Read arXiv Paper (karpathy/nanochat, 58k stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.

Who maintains Hla Typing?

ClawBio (a GitHub organization) maintains it in ClawBio/ClawBio, which has 1,154 GitHub stars. The repository holds 104 skills in this directory. The repository was last updated on October 7, 2026.

Source: ClawBio/ClawBio on GitHub. Facts on this page come from the repository at the commit we read; the author's words are quoted as theirs.

Install Hla Typing

Facts

At a glance

About this skill

Workflow steps

What it can do on your machine

Tool permissions

Runs code

Network

Credentials

Context cost

Safety

SKILL.md

Hla Typing

Trigger

Why This Exists

Core Capabilities

Scope

Input Formats

Workflow

CLI Reference

Demo

Algorithm / Methodology

Example Queries

Example Output

Output Structure

Dependencies

Gotchas

Safety

Agent Boundary

Integration with Bio Orchestrator

Maintenance

Citations

Files

Used in 1 other repository

Compare with similar skills

Similar skills

More from ClawBio/ClawBio

Related

Questions about Hla Typing