Version Compatibility

Reference examples tested with: bcftools 1.19+, picard 3.1+

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.

Reference Panels

"Set up reference panels for imputation" → Download, prepare, and manage reference panels (1000 Genomes, HRC, TOPMed) for genotype phasing and imputation, including population subsetting and format conversion.

• CLI: bcftools view -S panel_samples.txt for subsetting, bcftools norm for normalization

1000 Genomes Phase 3 (GRCh38)