Version Compatibility

Reference examples tested with: GATK 4.5+, samtools 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.

BWA-MEM2 Alignment

"Align reads with BWA" → Map DNA reads to a reference genome using BWA-MEM2, the standard aligner for whole-genome and exome sequencing.

• CLI: bwa-mem2 mem -t 8 ref.fa R1.fq R2.fq | samtools sort -o aligned.bam

Build Index