Variant Calling

Version Compatibility

Reference examples assume recent stable releases of the preferred tools, especially GATK-style and the other tools listed below.

Before using code or command patterns, verify installed versions match the environment:

• Python: python -c "import <module>; print(<module>.__version__)"
• CLI: <tool> --version
• If signatures differ, inspect the installed help or API and adapt the pattern instead of retrying unchanged.

Overview

Workflow for small-variant and structural-variant discovery, filtering, annotation, and interpretation from sequencing data.

When To Use This Skill