Version Compatibility

Reference examples tested with: GATK 4.5+, bcftools 1.19+, pysam 0.22+, samtools 1.19+

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.

Reference Operations

Generate consensus sequences and manage reference files using samtools.

"Prepare a reference genome" → Index the FASTA and create a sequence dictionary for downstream tools.

• CLI: samtools faidx ref.fa + samtools dict ref.fa -o ref.dict
• Python: pysam.FastaFile('ref.fa') (auto-uses .fai index)