Abstract: The present invention provides a method for detecting structural variations (SV) within genomes of single cells or population of single cells by integrating a three-layered information of sequencing read depth, read strand orientation and haplotype phase. The method of the invention can detect deletions, duplications, polyploidies, translocations, inversions, and copy number neutral loss of heterozygosity (CNN-LOH), and more. The method of the invention can fully karyotype a genome comprehensively, and may be applied in research and clinical approaches. For example, the methods of the invention are useful for analysing cellular samples of patients for diagnosing or aiding a diagnosis, in reproductive medicine to detect embryonic abnormalities, or during therapeutic approaches based on cellular therapies to quality control genetically engineered cells, such as in adoptive T cell therapy and others.