Fig. 3

Precision and recall of GeDi and MuTect for SNV detection at decreasing allele frequencies. We analysed the 35 simulated tumour-control paired targeted deep-sequencing datasets with MuTect, once using default settings, and GeDi, three times each time setting pMSS to 1, 2 and 4; in the legend, GeDi_mss1, GeDi_mss2, GeDi_mss4 refer respectively to the three GeDi analyses. For each analysis we then calculated the precision and recall attained by MuTect and GeDi. For each of the seven average allele frequencies, the arithmetic mean of the precision and recall attained by MuTect and GeDi (in each mode) across the five datasets (generated from the target sequences of hg19 chromosomes 1, 8, 9, 15, 22) are shown