Figure 1

Window filtering on HCC1143 sample’s RC profile. Visual assessment of the filtering performed by seqCNA on sample HCC1143. The profile (top) shows where the filtered windows lie within it. Mappability-filtered windows are marked as orange triangles; mapping quality-filtered, as magenta crosses; and trimming-filtered, as purple dots. The Venn diagram shows the overlaps among the windows filtered by the three applied filters. The plots on the right depict the density maps on which thresholds delimit the windows to be discarded based on the different filters.