SNPregator is a set of command-line tools used to collect aggregate data on Single Nucleotide Polymorphisms (SNPs) , as well as small Insertions and Deletions in the genome (INDELs). This data can be used to perform assocation tests like Fisher's Exact Test and Pearson's Chi-Square Test to determine if a SNP is associated with a particular group of samples being studied. The SNPs can also be filtered by these results, or by how density they are packed together, and can also be visualized graphically.