bio-long-read-sequencing-clair3-variants
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.
npx skills add majiayu000/claude-skill-registry --skill clair3-variants-gptomics-bioskills --agent claude-code
Same command for any agent — swap --agent for codex, cursor, copilot.
Weekly change comes from our own snapshots, not the repository page — it measures attention, not adoption.
# Clair3 Variant Calling ## Basic Usage ```bash # ONT variant calling run_clair3.sh \ --bam_fn=sample.bam \ --ref_fn=reference.fasta \ --threads=32 \ --platform=ont \ --model_path=${CONDA_PREFIX}/bin/models/ont \ --output=clair3_output # PacBio HiFi variant calling run_clair3.sh \ --bam_fn=sample.bam \ --ref_fn=reference.fasta \ --threads=32 \ --platform=hifi \ --model_path=${CONDA_PREFIX}/bin/models/hifi \ --output=clair3_output # Output: clair3_output/merge_output.vcf.gz ``` ## 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 | ```bash # List available models ls ${CONDA_PREFIX}/bin/models/ # Specify exact model run_clair3.sh \ --bam_fn=sample.bam \ --ref_fn=reference.fasta \ --model_path=${CONDA_PREFIX}/bin/models/r1041_e82_400bps_sup_v430 \ --output=clair3_out \ --threads=32 ``` ## Key Parameters | Parameter | Description | |-----------|-------------| | --platform | ont, hifi, or ilmn | | --model_path | Path to trained model | | --bed_fn | Restrict
- Basic Usage
- Platform-Specific Models
- Key Parameters
- Region-Specific Calling
- gVCF Output
- Phased Variant Calling
- Quality Filtering
- Python Wrapper
- Comparison with Other Callers
- Troubleshooting
- Docker Usage
- Related Skills
ONT variant calling
run_clair3.sh \
PacBio HiFi variant calling
List available models
ls ${CONDA_PREFIX}/bin/models/
Specify exact model
Call variants in specific regions
Call on non-human genomes (all contigs)
Generate gVCF for joint calling
Joint genotyping multiple samplesWhat does the bio-long-read-sequencing-clair3-variants skill do?
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.
How do I install it?
Run `npx skills add majiayu000/claude-skill-registry --skill clair3-variants-gptomics-bioskills --agent claude-code` — it drops the skill into your project so the agent can pick it up. Swap the --agent value for codex, cursor or copilot if you use one of those.
Where does this skill come from?
From majiayu000/claude-skill-registry, a repository with 534 stars. We read it straight from the repository tree rather than a submitted listing, so what you see here is what is actually published.
Is a popular skill a good skill?
Not necessarily. Stars measure attention, not adoption — a repository can trend for a week and be abandoned. That is why we show the weekly change from our own snapshots next to the total, instead of a single flattering number.