bio-workflows-cnv-pipeline

Version Compatibility

Reference examples tested with: CNVkit 0.9+, GATK 4.5+

Before using code patterns, verify installed versions match. If versions differ:

• CLI: <tool> --version then <tool> --help to confirm flags

If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying.

CNV Pipeline

"Detect copy number variants from my sequencing data" → Orchestrate CNVkit coverage analysis, segmentation, calling, visualization, and annotation for exome or targeted sequencing panels.

Complete workflow for detecting copy number variants from exome or targeted sequencing data.

Workflow Overview

BAM files (tumor/normal or germline)
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[1. Target Preparation] --> Create/access target BED
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[2. Coverage Calculation] --> Read depth per target
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[3. Reference Creation] --> Pool of normals
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[4. CNV Calling] --------> Log2 ratios, segmentation
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[5. Visualization] ------> Scatter plots, heatmaps
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[6. Annotation] ---------> Gene-level CNVs
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CNV calls with gene annotations

Primary Path: CNVkit

Step 1: Prepare Target Regions

# If using exome capture kit BED
cnvkit.py target capture_targets.bed \
    --annotate refFlat.txt \
    --split \
    -o targets.bed

# Access regions (off-target for WGS-like sensitivity)
cnvkit.py access genome.fa \
    -o access.bed

cnvkit.py antitarget targets.bed \
    --access access.bed \
    -o antitargets.bed

Step 2: Calculate Coverage

# For each sample
for bam in *.bam; do
    sample=$(basename $bam .bam)

    # Target coverage
    cnvkit.py coverage $bam targets.bed \
        -o coverage/${sample}.targetcoverage.cnn

    # Antitarget coverage
    cnvkit.py coverage $bam antitargets.bed \
        -o coverage/${sample}.antitargetcoverage.cnn
done

Step 3: Create Reference (Pool of Normals)

# From normal samples
cnvkit.py reference \
    coverage/normal*.targetcoverage.cnn \
    coverage/normal*.antitargetcoverage.cnn \
    --fasta genome.fa \
    -o reference.cnn

# Or flat reference (no normals available)
cnvkit.py reference \
    --fasta genome.fa \
    --targets targets.bed \
    --antitargets antitargets.bed \
    -o flat_reference.cnn