Version Compatibility

Reference examples tested with: 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.

Pileup Generation

Generate pileup data for variant calling and position-level analysis.

"Generate pileup from BAM" → Produce per-position read summaries showing depth, bases, and qualities.

• CLI: samtools mpileup -f ref.fa input.bam
• Python: bam.pileup(chrom, start, end) (pysam)