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.

Joint Calling

"Joint genotype my cohort samples" → Combine per-sample gVCFs into a single cohort callset with consistent genotyping across all sites, enabling VQSR and population-level analysis.

• CLI: gatk HaplotypeCaller -ERC GVCF → gatk GenomicsDBImport → gatk GenotypeGVCFs

Why Joint Calling?