bio-copy-number-cnvkit-analysis

npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-copy-number-cnvkit-analysis --agent claude-code

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

## Version Compatibility Reference examples tested with: GATK 4.5+, bedtools 2.31+ Before using code patterns, verify installed versions match. If versions differ: - Python: `pip show <package>` then `help(module.function)` to check signatures - 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. # CNVkit CNV Analysis **"Detect copy number variants from my exome data"** → Run a read-depth-based pipeline that normalizes on/off-target coverage against a reference, segments the log2 ratio profile, and calls gains/losses. - CLI: `cnvkit.py batch tumor.bam --normal normal.bam` ## Basic Workflow **Goal:** Run the complete CNVkit pipeline on a tumor-normal pair to detect copy number variants. **Approach:** Execute the batch command which wraps target/antitarget generation, coverage calculation, reference building, and segmentation into one step. ```bash # Complete pipeline for tumor-normal pair cnvkit.py batch tumor.bam \ --normal normal.bam \ --targets targets.bed \ --fasta reference.fa \ --output-reference my_reference.c

Complete pipeline for tumor-normal pair
cnvkit.py batch tumor.bam \
Step 1: Build reference from multiple normals (recommended)
cnvkit.py batch \
Step 2: Run on tumor samples using pre-built reference
cnvkit.py batch tumor1.bam tumor2.bam \
When no matched normal is available
For whole genome sequencing (no targets file)
Generate bedGraph: bedtools genomecov -ibam sample.bam -bg | bgzip > sample.bed.gz && tabix -p bed sample.bed.gz
cnvkit.py coverage sample.bed.gz targets.target.bed -o sample.targetcoverage.cnn