Clair Variant Caller (Claude Skill)

An agent skill that teaches Claude how to run the Clair suite of deep-learning variant callers for germline, somatic, mosaic, and long-read RNA variant detection.

   
Type Claude Skill
Supplier HKU-BAL
Availability GA
Pricing Free / OSS — Clair tools are BSD-3-Clause; skill wrapper distributed as-is (Unverified — no explicit SPDX license file on the skill repo)
Capabilities Read/Write — Claude invokes the Clair CLIs locally (Bash) over BAM/CRAM inputs and writes VCFs
Verified works · 2026-07-20
Security caution · 2026-07-20 — HKU-BAL/Clair-skills resolves, provenance matches, but no SPDX LICENSE on the skill repo, single-maintainer; no advisories

How to install

The skill is a SKILL.md (plus helper docs) that Claude reads; the underlying Clair callers must be installed separately (see Notes).

  • Claude Code — global install: 
    git clone https://github.com/HKU-BAL/Clair-skills.git ~/.claude/skills/clair-variant-caller
  • Claude Code — project-level install (clone into the repo you are working in): 
    git clone https://github.com/HKU-BAL/Clair-skills.git .claude/skills/clair-variant-caller

The skill resolves as /clair-variant-caller once cloned into a skills directory. No registration command is needed for skills — Claude loads them from the skills folder on the next session.

What it does

Wraps five tools from the Clair suite:

  • Clair3 — germline variant calling (DNA)
  • Clair3-RNA — variant calling from long-read RNA-seq
  • ClairS — somatic variant calling (paired tumor/normal)
  • ClairS-TO — somatic variant calling (tumor-only)
  • Clair-Mosaic — mosaic variant calling

The skill guides input preparation (BAM/CRAM + reference), model/platform selection (ONT, PacBio HiFi, Illumina), and command construction for each caller.

Primary use cases: germline SNP/indel calling, somatic variant calling (tumor/normal and tumor-only), mosaic variant detection, long-read RNA variant calling.

Notes

This skill provides procedural know-how only — the Clair binaries (Clair3, ClairS, etc.) and their model files must be installed on the host (typically via the per-tool conda/Docker instructions in the upstream Clair repos). The skill repo states it is “provided as-is for use with the Clair suite”; the Clair tools themselves are BSD-3-Clause licensed by HKU-BAL. For short-read germline calling via GATK see gatk-variant-calling.md; for variant annotation see snpeff-variant-annotation.md.

Sources

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