Bacterial genome-wide association studies (bGWAS) capture associations between genomic variation and phenotypic variation. Convergence based bGWAS methods identify genomic mutations that arise more often in the presence of phenotypic variation than is expected by chance. This work introduces hogwash, an open source R package that implements three algorithms for convergence based bGWAS. Hogwash additionally contains a novel grouping tool to perform gene- or pathway-analysis to improve power and increase convergence detection for related but weakly penetrant genotypes. To identify optimal use cases we applied hogwash to data simulated with a variety of phylogenetic signals and convergence distributions. These simulated data are publicly available and contain the relevant metadata regarding convergence and phylogenetic signal for each phenotype and genotype. Hogwash is available for download from GitHub.