Fig. 1

Flowchart of pipeline used to detect structural variants (SV). CNV copy number variants, RO reciprocal overlap, DEL deletions, DUP duplications, INV inversions. First, SV was detected separately by each tool within each sample through the integration software Parliament2. Second, filtering was applied at the software level, following the suggested criteria for each tool. Only SVs that passed all filters were retained and compared within the sample to retain common CNVs and INVs detected by the different tools. CNVs should share at least 90% of their sequence between the three tools, and INVs should share at least 90% of their sequence between Delly and Lumpy calls. Own work.