Version Compatibility

Reference examples tested with: bedtools 2.31+, numpy 1.26+, pandas 2.2+, 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.

Coverage Analysis

"Calculate sequencing coverage" → Compute per-base or per-region depth from BAM files to assess sequencing adequacy.

• CLI: bedtools genomecov -ibam input.bam, samtools depth input.bam
• Python: pybedtools.BedTool('input.bam').genome_coverage() (pybedtools)

Calculate coverage and depth across genomic regions using bedtools and pybedtools.