Version Compatibility

Reference examples tested with: bcftools 1.19+, bedtools 2.31+, pandas 2.2+

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.

BED File Basics

"Work with BED files" → Read, create, and manipulate genomic interval files in BED format (0-based, half-open coordinates).

• Python: pybedtools.BedTool('file.bed') (pybedtools)
• CLI: bedtools commands

BED (Browser Extensible Data) format stores genomic intervals. Uses 0-based, half-open coordinates.