Fig. 1

Overview of the SV genotyping workflow implemented in Paragraph. The illustration shows the process to genotype a blockwise sequence swap. Starting from an entry in a VCF file that specifies the SV breakpoints and alternative allele sequences, Paragraph constructs a sequence graph containing all alleles as paths of the graph. Colored rectangles labeled FLANK, ALTERNATIVE, and REFERENCE are nodes with actual sequences, and solid arrows connecting these nodes are edges of the graph. All reads from the original, linear alignments that aligned near or across the breakpoints are then realigned to the constructed graph. Based on alignments of these reads, the SV is genotyped as described in the “Methods” section