Version Compatibility

Reference examples tested with: picard 3.1+, 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.

Duplicate Handling

"Remove PCR duplicates from my BAM file" → Mark or remove duplicate reads using the fixmate-sort-markdup pipeline to prevent duplicate bias in variant calling.

• CLI: samtools fixmate, samtools markdup (samtools)
• Python: pysam.fixmate(), pysam.markdup() (pysam)

Mark and remove PCR/optical duplicates using samtools.