Abstract: We describe an extension to our variant calling tool, Oc- topus (https://github.com/luntergroup/octopus), for single-cell DNA sequencing data. Octopus jointly geno- types cells from a lineage, accounting for amplification stochasticity and sequencing error with a haplotype-based Bayesian model. Octopus is considerably more accurate at genotyping single cells than existing methods.