of choosing suitable statistical models. Moreover, comparing with VarScan2, which conducts the Fisher’s exact test for each targeted location on paired normal-tumor sequencing data, the significance of applying the correct reference error model is exemplified by higher recalls as well as precisions for 0.5 % and 1 % frequency SNVs. In theory, for low frequency SNV loci, VarScan2 treated the sequencing reads with non-reference bases from normal as the background error, which is essentially point estimation based on one location. Whereas PSEM collectively considers all loci with similar context features and thus is able to generate more accurate error estimation.
