Accurate genotyping of DNA from a single cell is required for applications such as de novo mutation detection, linkage analysis and lineage tracing. However, achieving high precision genotyping in the single cell environment is challenging due to the errors caused by whole genome amplification. Two factors make genotyping from single cells using single nucleotide polymorphism (SNP) arrays challenging. The lack of a comprehensive single cell dataset with a reference genotype and the absence of genotyping tools specifically designed to detect noise from the whole genome amplification step. Algorithms designed for bulk DNA genotyping cause significant data loss when used for single cell applications.