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bio-long-read-sequencing-clair3-variants
Maintainer FreedomIntelligence · Last updated April 1, 2026
Deep learning-based variant calling from long reads using Clair3 for SNPs and small indels. Use when calling germline variants from ONT or PacBio alignments, particularly when high accuracy is needed for clinical or research applications.
Original source
FreedomIntelligence/OpenClaw-Medical-Skills
https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-long-read-sequencing-clair3-variants
- Maintainer
- FreedomIntelligence
- License
- MIT
- Last updated
- April 1, 2026
Skill Snapshot
Key Details From SKILL.md
Key Notes
- CLI: run_clair3.sh --bam_fn=sample.bam --ref_fn=ref.fa --platform=ont.
- Call variants from my long-read data" → Use deep learning to identify germline SNPs and small indels from ONT or PacBio aligned reads with high accuracy. CLI: run_clair3.sh --bam_fn=sample.bam --ref_fn=ref.fa --platform=ont.
- run_clair3.sh \ --bam_fn=sample.bam \ --ref_fn=reference.fasta \ --threads=32 \ --platform=ont \ --model_path=${CONDA_PREFIX}/bin/models/ont \ --output=clair3_output.
Source Doc
Excerpt From SKILL.md
PacBio HiFi variant calling
run_clair3.sh
--bam_fn=sample.bam
--ref_fn=reference.fasta
--threads=32
--platform=hifi
--model_path=${CONDA_PREFIX}/bin/models/hifi
--output=clair3_output
Platform-Specific Models
| Platform | Model | Recommended Coverage |
|---|---|---|
| ONT R10 | r1041_e82_400bps_sup_v430 | 30-60x |
| ONT R9 | r941_prom_sup_g5014 | 30-60x |
| PacBio HiFi | hifi | 20-40x |
| PacBio CLR | - | Use PEPPER-Margin-DeepVariant |
## List available models
ls ${CONDA_PREFIX}/bin/models/
Use cases
- Use when calling germline variants from ONT or PacBio alignments, particularly when high accuracy is needed for clinical or research applications.
Not for
- Do not rely on this catalog entry alone for installation or maintenance details.
Upstream Related Skills
- variant-calling/bcftools-basics - VCF manipulation
- variant-calling/filtering-best-practices - Quality filtering
- long-read-sequencing/long-read-qc - Input quality control
- long-read-sequencing/long-read-alignment - Mapping with minimap2
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