Fig. 2: Landscape of mutations overlap by caller, sample and cancer type.
From: Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples
a UpSetR41 plot shows the variant calling set intersection by caller. The y-axis indicates set intersection size and the x-axis uses a connected dot plot to indicate which sets are considered. Only the largest 27 intersecting sets are shown. Two insets of the UpSetR plot highlight a classic Euler diagram (left), which indicates the total number of overlapping mutations. A set-size bar chart (right) illustrates the total number of mutations considered from each caller. The concordance set indicates the agreement between WES and WGS. Indel callers are indicated with an asterisk. b A scatter plot shows the amount of concordance by sample by calculating the fraction of matched variants divided by the total number of mutations made by MC3 exome sequencing and PCAWG whole genome sequencing (x and y-axis, respectively) below the total fraction of samples within each quadrant. Each point within the plot is related to tumor portion data collected from the TCGA barcode ID. c As shown above, this box plot separates panel b by cancer types (blue considers all MC3 variants, and red boxes indicate all PCAWG variants). Sample sizes are displayed for each cancer; points indicate samples that extend past 1.5 times the interquartile range; and horizontal bars within each box and whisker indicates median matched mutation fraction.
