Agent skill

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.

View SKILL.md on GitHub Repository
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Install this agent skill to your Project

npx add-skill https://github.com/majiayu000/claude-skill-registry/tree/main/skills/data/clair3-variants

SKILL.md

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 calling to regions
--include_all_ctgs Call on all contigs (not just chr1-22,X,Y)
--no_phasing_for_fa Disable phasing
--gvcf Output gVCF format
--qual Minimum variant quality (default: 2)

Region-Specific Calling

bash
# Call variants in specific regions
run_clair3.sh \
    --bam_fn=sample.bam \
    --ref_fn=reference.fasta \
    --bed_fn=target_regions.bed \
    --threads=32 \
    --platform=ont \
    --model_path=${CONDA_PREFIX}/bin/models/ont \
    --output=clair3_targeted

# Call on non-human genomes (all contigs)
run_clair3.sh \
    --bam_fn=sample.bam \
    --ref_fn=reference.fasta \
    --include_all_ctgs \
    --threads=32 \
    --platform=hifi \
    --model_path=${CONDA_PREFIX}/bin/models/hifi \
    --output=clair3_all_contigs

gVCF Output

bash
# Generate gVCF for joint calling
run_clair3.sh \
    --bam_fn=sample.bam \
    --ref_fn=reference.fasta \
    --gvcf \
    --threads=32 \
    --platform=ont \
    --model_path=${CONDA_PREFIX}/bin/models/ont \
    --output=clair3_gvcf

# Joint genotyping multiple samples
bcftools merge sample1.g.vcf.gz sample2.g.vcf.gz -o cohort.vcf.gz

Phased Variant Calling

bash
# With phasing information (requires haplotagged BAM)
run_clair3.sh \
    --bam_fn=haplotagged.bam \
    --ref_fn=reference.fasta \
    --enable_phasing \
    --longphase_for_phasing \
    --threads=32 \
    --platform=ont \
    --model_path=${CONDA_PREFIX}/bin/models/ont \
    --output=clair3_phased

Quality Filtering

bash
# Filter by quality score
bcftools view -i 'QUAL>20' clair3_output/merge_output.vcf.gz -Oz -o filtered.vcf.gz

# Filter by genotype quality
bcftools view -i 'GQ>30' clair3_output/merge_output.vcf.gz -Oz -o high_gq.vcf.gz

# SNPs only
bcftools view -v snps clair3_output/merge_output.vcf.gz -Oz -o snps.vcf.gz

# Indels only
bcftools view -v indels clair3_output/merge_output.vcf.gz -Oz -o indels.vcf.gz

Python Wrapper

python
import subprocess
from pathlib import Path

def run_clair3(bam, reference, output_dir, platform='ont', model_path=None,
               threads=32, bed=None, gvcf=False, include_all_ctgs=False):
    if model_path is None:
        import os
        conda_prefix = os.environ.get('CONDA_PREFIX', '')
        model_path = f'{conda_prefix}/bin/models/{platform}'

    cmd = [
        'run_clair3.sh',
        f'--bam_fn={bam}',
        f'--ref_fn={reference}',
        f'--threads={threads}',
        f'--platform={platform}',
        f'--model_path={model_path}',
        f'--output={output_dir}'
    ]

    if bed:
        cmd.append(f'--bed_fn={bed}')
    if gvcf:
        cmd.append('--gvcf')
    if include_all_ctgs:
        cmd.append('--include_all_ctgs')

    subprocess.run(cmd, check=True)
    return Path(output_dir) / 'merge_output.vcf.gz'

def filter_variants(vcf, output, min_qual=20, variant_type=None):
    cmd = ['bcftools', 'view', '-i', f'QUAL>{min_qual}']
    if variant_type:
        cmd.extend(['-v', variant_type])
    cmd.extend([vcf, '-Oz', '-o', output])
    subprocess.run(cmd, check=True)
    subprocess.run(['bcftools', 'index', '-t', output], check=True)
    return output

# Example
vcf = run_clair3('sample.bam', 'ref.fa', 'clair3_out', platform='hifi', threads=48)
snps = filter_variants(str(vcf), 'snps_q20.vcf.gz', min_qual=20, variant_type='snps')

Comparison with Other Callers

Caller Best For Speed Accuracy
Clair3 ONT/HiFi germline Fast High
DeepVariant HiFi, Illumina Medium Very high
PEPPER-DV ONT (integrated) Slow Very high
Longshot ONT SNPs Fast Good

Troubleshooting

Issue Solution
Missing model Download from Clair3 releases or use conda models
Low call rate Check coverage; increase --qual threshold
Slow performance Reduce --threads or use --bed_fn for targeted calling
Wrong variants on non-human Use --include_all_ctgs

Docker Usage

bash
# Using Docker
docker run -v /data:/data \
    hkubal/clair3:latest \
    /opt/bin/run_clair3.sh \
    --bam_fn=/data/sample.bam \
    --ref_fn=/data/reference.fasta \
    --threads=32 \
    --platform=ont \
    --model_path=/opt/models/ont \
    --output=/data/clair3_output

# Singularity
singularity exec clair3.sif run_clair3.sh \
    --bam_fn=sample.bam \
    --ref_fn=reference.fasta \
    --threads=32 \
    --platform=ont \
    --model_path=/opt/models/ont \
    --output=clair3_output

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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