Version Compatibility

Reference examples tested with: GATK 4.5+, bcftools 1.19+

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 Variant Calling

GATK HaplotypeCaller is the gold standard for germline variant calling. This skill covers the GATK Best Practices workflow.

Prerequisites

BAM files should be preprocessed:

1. Mark duplicates
2. Base quality score recalibration (BQSR) - optional but recommended