Integration of SVs and CNVs for cancer genomes via karyotype-graph integration. (A) Haplotype constraint groups determined via uninterrupted SVs (uSVs) and long ONT and/or PacBio reads spanning multiple SVs. Distribution over the number of haplotype constraint groups inferred with only uSVs, and various combinations of uSVs and short/long reads in patient 51. (B) Workflow of the reconstruction of haplotype-specific cancer karyotype graphs (RCK) method with allele-specific copy number profiles on large fragments, resolved SV call set, and inferred haplotype constraint groups as inputs. (C) Circos plot of the CNVs and SVs from karyotype graph inferred by RCK for patient 51 with HATCHet segment copy number (CN) input. The top two tracks correspond to fractions x/y of the total length x of either amplified (CN ≥ 1) or deleted (CN = 0) fragments over the y = 5 × 106 long windows. Breakend track shows the total number (with 590 being the maximum value shown) of breakends inferred by RCK as being present.
