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.

BAM Statistics

"Get alignment statistics and coverage from my BAM file" → Generate read counts, mapping rates, per-chromosome statistics, depth profiles, and coverage summaries.

• CLI: samtools flagstat, samtools stats, samtools depth, samtools coverage (samtools)
• Python: pysam.AlignmentFile with pileup() and get_index_statistics() (pysam)

Generate alignment statistics using samtools and pysam.