Version Compatibility

Reference examples tested with: bcftools 1.19+

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

• 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.

Haplotype Phasing

"Phase my genotypes into haplotypes" → Resolve which alleles are inherited together on each chromosome for downstream imputation, HLA typing, or population genetic analyses.

• CLI: java -jar beagle.jar gt=input.vcf out=phased (Beagle 5.4)
• CLI: shapeit4 --input input.vcf --output phased.vcf (SHAPEIT)

Beagle 5.4 Phasing (Recommended)