Version Compatibility

Reference examples tested with: 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.

PLINK Basics

"Convert my VCF to PLINK format and run QC" → Handle PLINK file format conversions (VCF, BED/BIM/FAM, PED/MAP) and apply standard genotype QC filters for MAF, genotyping rate, and HWE.

• CLI: plink2 --vcf input.vcf --make-bed for format conversion
• CLI: plink2 --maf 0.01 --geno 0.05 --hwe 1e-6 for QC filtering

File formats, conversion, and quality control filtering with PLINK 1.9 and 2.0.