Clair Variant Caller Skill

An agent skill for the Clair suite of variant callers. Provides intelligent model selection, command generation, and troubleshooting for germline, somatic, mosaic, and RNA-seq variant calling from long-read and short-read sequencing data.

Supported Tools

Tool	Repository	Purpose
Clair3	HKU-BAL/Clair3	Germline variant calling (DNA)
Clair3-RNA	HKU-BAL/Clair3-RNA	Variant calling from long-read RNA-seq
ClairS	HKU-BAL/ClairS	Somatic variant calling (paired tumor/normal)
ClairS-TO	HKU-BAL/ClairS-TO	Somatic variant calling (tumor-only)
Clair-Mosaic	HKU-BAL/Clair-Mosaic	Mosaic variant calling

Installation

This skill follows the Agent Skills open standard and works with Claude Code, Codex CLI, and Cursor.

Claude Code

# Global (available in all projects)
git clone https://github.com/HKU-BAL/Clair-skills.git ~/.claude/skills/clair-variant-caller

# Project-level
git clone https://github.com/HKU-BAL/Clair-skills.git .claude/skills/clair-variant-caller

Codex CLI

# Global
git clone https://github.com/HKU-BAL/Clair-skills.git ~/.codex/skills/clair-variant-caller

# Project-level
git clone https://github.com/HKU-BAL/Clair-skills.git .codex/skills/clair-variant-caller

Cursor

# Global
git clone https://github.com/HKU-BAL/Clair-skills.git ~/.cursor/skills/clair-variant-caller

# Project-level
git clone https://github.com/HKU-BAL/Clair-skills.git .cursor/skills/clair-variant-caller

Cursor also auto-discovers skills from ~/.claude/skills/ and ~/.codex/skills/.

Usage

The skill activates automatically when you mention variant calling, Clair tools, or provide BAM/FASTQ files. You can also invoke it explicitly:

• Claude Code: /clair-variant-caller
• Codex CLI: $clair-variant-caller
• Cursor: /clair-variant-caller

Example prompts

I have a BAM file at /data/sample.bam, help me call germline variants.

Call somatic variants from ONT R10.4.1 5kHz tumor-only data at /data/tumor.bam.

My data was basecalled with Dorado v5.2.0 SUP, which model should I use?

Benchmark my Clair3-RNA results against GIAB truth set.

Skill Structure

clair-variant-caller/
  SKILL.md              # Main skill file (model catalogs, workflows, logic)
  templates/
    clair3-command.sh         # Germline calling template
    clair3-rna-command.sh     # RNA-seq calling template
    clairs-command.sh         # Paired tumor/normal template
    clairs-to-command.sh      # Tumor-only template
    clair-mosaic-command.sh   # Mosaic calling template
  references/
    model-selection.md        # Model catalog details
    tool-selection.md         # Tool decision tree
    preprocessing.md          # FASTQ-to-BAM alignment guide
    analysis.md               # Post-processing, filtering, benchmarking
    file-inspection.md        # BAM inspection commands
    setup.md                  # Installation (Docker/Singularity/Conda)
  docs/
    quick-start.md            # Getting started guide
    troubleshooting.md        # Common issues and solutions

License

This skill is provided as-is for use with the Clair suite of tools. The Clair tools themselves are licensed under BSD 3-Clause by HKU-BAL.