PLINK 1.9 handles binary .bed files and autoconverts other formats. Supports VCF BCF Oxford and 23andMe inputs. Performs case-control and quantitative trait association tests. Computes allele frequencies missingness HWE and relatedness. Runs PCA clustering MDS and distance matrices. Executes logistic linear regression with covariates. Supports epistasis set-based tests and meta-analysis. Generates GRM for heritability estimation. Filters by MAF geno mind and ranges. Reports LD r r2 blocks and clumping. Handles X Y MT chromosomes properly. Fixes numerous bugs in merging filtering and regression. Imports dosage data for association. Exports to multiple formats including VCF gzipped. Optimizes for multithreading and large datasets.