Fig. 4: Performance of the tested methods on the HGSVC2 benchmark.

Sensitivity and precision for deletions (a) and tandem duplications (b) in the HGSVC2 catalogue. Each sample is a dot, its x coordinate is the sensitivity while its y coordinate is the precision. SurVIndel2 has higher sensitivity and precision than the other methods. c Sensitivity of the methods in predicting deletions in HG002, stratified by supporting evidence. Split reads (SR)-supported deletions are relatively easy for all methods, although SurVIndel2 has a clear advantage. However, SurVIndel2 is the only method that can detect most deletions with strong hidden split reads (HSR) support. d For tandem duplications, existing methods perform poorly even for SR-supported events. SurVIndel2 can detect nearly twice as many duplications as existing methods that are supported by split and hidden split reads.