Fig. 1

Examples of ambiguities resulting from the description of genomic rearrangements via basic SV. A shows a situation, where a duplication and an inversion correspond to three different outcomes, which are depicted by diagrammatic dot-plots (for a description of dot-plots and their diagrammatic representation see Additional file 2). Each outcome can be uniquely represented by a graph and its folded adjacency matrix. Here we show simplified versions of the graphs and their folded adjacency matrices merely. The unfolded matrices as well as the full graphs for all examples are given in Additional file 3. For testing SV callers that report genomic rearrangements via basic SV, such as Sniffles and Delly, we simulate 100 × coverage of error-free alignments for all cases with a read length of 1000 nt for long reads and 250 nt for paired-end short reads. B displays an example, where different rearrangements via basic SVs lead to equal outcomes. Here, a pair of inversions is equal to a duplication followed by two deletions and an inversion. As for A, the corresponding graph, folded adjacency matrix, and output of real-world SV callers are shown for both examples. Additional file 3 gives an analogous example, where a duplication followed by two inversions leads to the same outcome as two duplications followed by one inversion