System and Method for Correlated Error Event Mitigation for Variant Calling

Methods, systems, and apparatus, including computer programs for improving the accuracy of a variant call by accounting for indications of correlated error events. In one aspect, a method may include actions of accessing a pileup of sequence reads aligned to a first region of a reference genome, obtaining information describing one or more characteristics of each of the plurality of reads of the pileup, providing one or more inputs to a probability model describing the one or more characteristics of the plurality of reads of the pileup, wherein the probability model is configured to determine a score, for each hypothesis of one or more hypotheses selected based on the one or more inputs, that indicates whether each hypothesis is true, obtaining output information for each of the one or more hypotheses, and determining, based on the obtained output information, a likelihood that a true variant exists at the first position.