Fig. 3

Structural variant initial and high-confidence call set. a Bar chart plot displays BNDs, DELs, DUPs, INSs, INVs, and TRA on all chromosomes from initial call set. b Bar chart plot displays BNDs, DELs, DUPs, INSs, INVs, and TRA on all chromosomes from high-confidence call set. c Upset plot to display the number of SV overlap between the different NGS platforms. The blue horizontal bars on the left side show the total number of SVs in the specific NGS platform, black dots on the pink bars denote total SVs called in each platform. The top black vertical bars display the total concordance calls among the different platforms. d Density plot for SV size distributions for Deletion events (top panel) and Duplication events (bottom panel). The y-axis denotes log10 scale of number of SVs; the x-axis denotes the SV size bin from 50bp to 20Mb. e Circos plot visualization of results from the HATCHet + RCK analysis from the matched tumor/normal (HCC1395 and HCC1395BL) WGS analysis. The amplification track (CN > 1, red) and deletion track (CN < 1, blue) show the fraction of the amplified or deleted regions as reported by RCK. The breakpoint bar plot shows the number of novel adjacency (structural variant) breakpoints that start or end within a chromosomal region (max = 128). The center chord diagram shows the start and end points for all inter-chromosomal transversion events (n = 122). All structural variants shown are present in the consensus call set. Chromosomal regions for the amplification, deletion, and structural variant breakpoint tracks are binned into 5 megabase windows