bio-workflows-cnv-pipeline

npx skills add BioTender-max/awesome-bio-agent-skills --skill cnv-pipeline --agent claude-code

Same command for any agent — swap --agent for codex, cursor, copilot.

## 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) | v [1. Target Preparation] --> Create/access target BED | v [2. Coverage Calculation] --> Read depth per target | v [3. Reference Creation] --> Pool of normals | v [4. CNV Calling] --------> Log2 ratios, segmentation | v [5. Visualization] ------> Scatter plots, heatmaps | v [6. Annotation] ---------> Gene-level CNVs | v CNV calls with gene annotations ``` ## Primary Path: CNVkit ### Step 1: Prepare Target Regions ```bash # If using exome capture ki

If using exome capture kit BED
cnvkit.py target capture_targets.bed \
Access regions (off-target for WGS-like sensitivity)
cnvkit.py access genome.fa \
cnvkit.py antitarget targets.bed \
For each sample
for bam in *.bam; do
cnvkit.py coverage $bam targets.bed \
cnvkit.py coverage $bam antitargets.bed \
done