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.