The SNPman program calls the genotypes of single nucleotide polymorphisms (SNP) from TaqMan allelic discrimination assays. It utilizes the fluorescence data collected over the whole PCR run, rather than relying on the end point fluorescence measurements that is the basis of the genotype calling process in most software solutions sold with the real-time instruments. This inspection of run data facilitates genotype calls in difficult sample sets, especially in those containing various concentrations of DNA or inhibitors, as indicated by results of a reanalysis of 3738 genotyping samples. The program works with data from three different widely used PCR instruments.