Fig. 5

Validation in clinical samples. In 10 normal samples for which two or three sets of WES data from independent libraries were available we ran the different pipelines according to Fig. 1 using one replicate as ’tumour’ and the other as ’normal’ and vice versa, for a total of 28 comparisons (a, b). In this setting, all called mutations are treated as false positives. Boxplots represent FPR/Mb distributions for the 28 comparisons as a function of the different pipelines applied to identify somatic SNVs (a) or indels (b). The same set of analysis pipelines was applied to a breast cancer tumour sample for which two sets of WES data from independent libraries (R1 and R2) as well as matched normal WES data were available (c, d). The percentage (x-axis) and the total number (y-axis) of overlapping calls in the two replicates are plotted in c for R1 and d for R2. Sequencing coverage was 52× for R1 and 79× for R2