Fig. 4

Comparison of Calls of True Somatic Variants and True Values of Variants Called Somatic. The graphs on the left shows the calls of LumosVar (bottom bar in pair) compared to filtering approach (top bar in pair) in calling true somatic variants. The size of the yellow portions of the bars indicate the number of true somatic variants falsely called germline heterozygotes or homozygous, the grey represents true somatic variants that were filtered on quality or not detected as variants, and the blue represents true positive somatic calls. We can see that the filtering approach has better sensitivity (mean TPR 87%, range 78%–96%) compared to the tumor only caller (mean TPR 52%, range 27%–62%). The graphs on the right shows the number of somatic calls by the LumosVar (bottom bar in pair) compared to the filtering approach (top bar in pair) that are truly germline private heterozygous (red), germline heterozygous database variants (pink), homozygous (grey) or truly somatic (blue). We can see that the tumor only caller has better precision (mean PPV 75%, range 56%–89%) compared to the filtering approach (mean PPV 35%, range 19%–55%). The top pair of panels shows the comparison for eight of the nine evaluation samples. The middle of panels shows the comparison for an in-silico dilution series preformed using the ninth evaluation sample (GBMEA1), while the bottom panel shows a down-sampling experiment on the same sample