Version Compatibility

Reference examples tested with: matplotlib 3.8+, numpy 1.26+, 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.

Linkage Disequilibrium

"Calculate LD between my variants" → Compute pairwise LD statistics (r², D'), prune correlated variants for independent sets, and identify haplotype blocks from genotype data.

• CLI: plink2 --r2 for LD calculation, --indep-pairwise for pruning
• Python: allel.rogers_huff_r() for windowed LD in scikit-allel

Calculate LD statistics, prune correlated variants, and identify haplotype blocks.