Extended Data Figure 1.

SV mapping pipeline. SV are detected within each sample using LUMPY. Breakpoint probability distributions are used to merge and refine the position of detected SV within a cohort, followed by parallelized re-genotyping, and copy number annotation. Samples are merged into a single cohort-level VCF file, variant types reclassified, and genotypes refined with svtools using the combined breakpoint genotype and read-depth information. Finally, sample-level QC and variant confidence scoring is conducted to produce the final callset.