Version Compatibility

Reference examples tested with: 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.

GATK CNV Workflow

"Call CNVs using GATK best practices" → Collect read counts, build a panel of normals, denoise tumor coverage, model segments with allelic counts, and call copy ratio states.

• CLI: gatk CollectReadCounts → gatk DenoiseReadCounts → gatk ModelSegments → gatk CallCopyRatioSegments

Somatic CNV Workflow Overview