Fig. 3

Performance comparison for indel detection with 100-bp simulated reads. Recall (upper panels) and precision (lower panels) are evaluated for ScanIndel, GATK HaplotypeCaller, Pindel, Platypus, Scalpel, Delly and FermiKit. Smoothed histograms (100-bp bins) showed the comparison on simulated data of 10×, 20× and 50× mean coverage for detecting 1000 deletions and 1000 insertions, one each from the size range 1 bp to 1 kb. Precision is not calculated if a zero denominator (TP + FP = 0) is given by the method