Fig. 1

Precision and sensitivity of Breakdancer, Pindel and overlap methods for the detection of structural variations in different simulation scenarios. a Precision of each method; b sensitivity of each method; BD Breakdancer, PD Pindel, OV overlap method, DEL deletions, INV inversions, DUP duplications. BCE base calling error rate, MIX mix scenario with SNP% = 0.01, SNP rate = 0.008 and half of the SV falling into repetitive regions. Precision is defined as the average number of true positives divided by the average number of total calls made by each program. Sensitivity is defined as the average number of true positives divided by the average number of actual variants in the simulations