Abstract: Disclosed is a method of detecting a genomic structural variation based on k-mer set in a reference genome by means of a computer apparatus, the method including receiving sample sequence data, comparing the sample sequence data to k-mer set in reference genome data to determine at least one k-mer read that is not included in the reference genome data among reads of the sample sequence data, determining a breakpoint and a candidate region of a structural variation by mapping the at least one k-mer read to standard reference genome data, and predicting a structural variation type for the sample sequence data on the basis of a sequence mapping pattern and the breakpoint corresponding to the mapping result.