Fig. 4.

Filtering of NeoSeq SVs using AF cutoffs. The fraction of NeoSeq proband SV calls, per SVTYPE, that are filtered by using the Max_AF annotation added by SVAFotate and a range of AF cutoff values. SVTYPEs are abbreviated as follows: deletions (DELs), duplications (DUPs), inversions (INVs), and insertions (INSs). Plots on the left are SV calls derived from Smoove while the plots on the right are from Manta. Lines that are colored represent the resulting filtered SVs using the Max_AF annotation generated using the provisional BED file, while the gray lines represent the filtered SVs using the Max_AF annotation created by the custom NeoSeq BED file. Each line has the maximum and minimum amount of filtered SVs observed across all 22 NeoSeq cases analyzed plotted as a shadow surrounding the line