Performance comparison for structural variations in a simulated heterogeneous tumor cell population. To measure SV detection performance in the case of a heterogeneous tumor sample, we created a mock tumor genome by embedding 5,516 non-overlapping deletions identified by the 1000 Genomes Project into the human reference genome (build 37). Sequence reads were simulated separately from both the ‘tumor’ genome and the unaltered reference genome. We then mixed reads from both genomes in varying proportions to obtain simulated datasets representing a tumor cell population with different SV allele frequencies. Sequencing coverage levels are shown above each plot, and SV allele frequencies are shown beneath each plot. (A) Sensitivity for detecting SVs at varying allele frequencies and coverage levels. In all cases, LUMPY was more sensitive than GASVPro, DELLY, and Pindel, and showed a marked improvement when the coverage of the ‘tumor’ genome was low owing to either low sequence coverage or low SV allele frequency. In general, to achieve the same level of sensitivity as LUMPY, the other tools required twice the evidence from the ‘tumor’ genome. pe, paired-end; rd, read-depth; sr, split-read. (B) The FDRs for each tool at varying allele frequencies and coverage levels. The FDR for LUMPY was better than all other tools in all cases, with a notable improvement at lower SV allele frequencies. (C) The change in sensitivity when considering two SV detection signals versus a single signal alone is shown for the three tools at 40X coverage and at different SV allele frequencies. At low SV allele frequencies (for example, 5%), LUMPY’s use of two signals (that is, pe + sr) has a super-additive effect on sensitivity relative to either signal alone (that is, pe or sr), whereas the sensitivity of GASVPro and DELLY was either unchanged or modestly improved with one signal versus two.