Version Compatibility

Reference examples tested with: bcftools 1.19+, 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.

Genotype Imputation

"Impute missing genotypes using a reference panel" → Fill in untyped variants by leveraging LD patterns from a reference panel to increase variant density for GWAS or cross-platform harmonization.

• CLI: java -jar beagle.jar gt=input.vcf ref=panel.vcf out=imputed
• CLI: minimac4 --refHaps panel.m3vcf --haps input.vcf --prefix imputed

Beagle Imputation