Extended Data Fig. 9 |. SV Agreement between Callers and Instruments.

(a) Insights into SV variability by caller. First the strategy used to examine SV caller variability after stratifying for platforms, replicates and centers variability; next the SV call set sizes and overlap with the GIAB SV call set for the SV caller variability set of HG002; finally the types and sizes of SVs in the SV caller variability set of HG002 (translocations are set to size 50 by default in the SURVIVOR parameters for visualization purposes). (b) Insights into SV variability by platform. Diagrams utilize sequencing runs from HiSeqX10, HiSeq2000 and HiSeq4000 while the final two characterize all platforms available. First the strategy used to examine platform variability after stratifying for SV callers, centers and replicates variability; next, SV call set sizes and overlaps with the GIAB SV call set for the platform variability SV call set of HG002; next, types and sizes of SVs in the platform variability SV call set of HG002. Final two panels include HiSeqX10, HiSeq2000, HiSeq4000, NovaSeq, BGI and MGI for visualization purposes. The NovaSeq, BGI and MGI SV call sets were not integrated into the analyses strategy because sequencing runs with replicates for each sample at different centers on different platforms were not available. On top, SV call set sizes and overlap with the GIAB SV call set for the platform variability SV call set of HG002. Below, types and sizes of SVs in the platform variability SV call set of HG002. (Translocations are set to size 50 by default in the SURVIVOR parameters for visualization purposes).