New technologies capable of measuring chromatin state alongside other data modalities at single-cell resolution are now being rapidly developed. These include the development of assays that measure DNA accessibility data alongside mitochondrial genome sequence15,16,43. As the mitochondrial genome mutates at a much higher rate than the nuclear genome and mitochondrial mutations are inherited over cell divisions, measuring mitochondrial genome sequences in single cells can be informative in reconstructing clonal cell relationships15,16,43. These experiments therefore provide an opportunity to study DNA accessibility differences between or within clonal groups of cells. To facilitate joint analysis of these datasets, we developed computational methods to enable identification of informative mitochondrial variants, calculation of mitochondrial variant allele frequencies and clonal cell clustering within the Signac framework.
