Fig. 4

Concordance between ConanVarvar, CNVnator, Control-FREEC and Manta on the test dataset. Colour indicates the total number of false positives (red) and true positives (green). Only 4 variants were correctly identified by all tools. The remaining 9 true positives were reported only by ConanVarvar, CNVnator and Control-FREEC. Variants smaller than 50 kb in Manta’s output were excluded. As CNVnator and CNVpytor are different implementations of the same algorithm and have almost identical performance in terms of true and false positives, only CNVpytor’s calls are shown