Version Compatibility

Reference examples tested with: bedtools 2.31+, pandas 2.2+, pybedtools 0.9+, pysam 0.22+

Before using code patterns, verify installed versions match. If versions differ:

• Python: pip show <package> then help(module.function) to check signatures
• R: packageVersion('<pkg>') then ?function_name to verify parameters
• 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.

CNV Annotation

"Annotate my CNV calls with gene names" → Overlap CNV segments with gene annotations, clinical databases, and pathway information to identify affected genes and assess clinical significance.

• CLI: bedtools intersect -a cnvs.bed -b genes.bed
• Python: pybedtools.BedTool().intersect()

Annotate with Gene Names (bedtools)