Recent advances in molecular biology and microfluidics have enabled us to individually sequence the molecular contents of thousands of single cells using single-cell technology. Innovative technologies for single nucleotide variants (SNV) and indel analysis allow researchers to explore single-cell biology by simultaneously identifying the mutation profile within clonal populations, detect f rare subclones, and unambiguous determination of zygosity. These datasets promise to transform our understanding of cellular diversity, but the scale and complexity pose new bottlenecks for data processing and interpretation.