Version Compatibility

Reference examples tested with: bcftools 1.19+, 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.

Imputation QC

"Filter my imputed genotypes by quality" → Assess imputation accuracy using INFO/R2 scores, filter low-quality imputed variants, and validate against known genotypes before downstream GWAS.

• CLI: bcftools query -f '%CHROM %POS %INFO/R2\n' to extract quality scores
• Python: pandas for R2 distribution analysis and threshold selection

Extract INFO Scores