Version Compatibility

Reference examples tested with: 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.

Alignment Sorting

Sort alignment files by coordinate or read name using samtools and pysam.

"Sort a BAM file" → Reorder reads by genomic coordinate (for indexing/variant calling) or by name (for paired-end processing).

• CLI: samtools sort -o sorted.bam input.bam
• Python: pysam.sort('-o', 'sorted.bam', 'input.bam')