Fig. 3

Exonic deletion in the HGSVC dataset correctly genotyped by vg. a Visualization of the HGSVC graph as augmented by reads aligned by vg at a locus harboring a 51-bp homozygous deletion in the UTR region of the LONRF2 gene. At the bottom, a horizontal black line represents the topologically sorted nodes of the graph. Black rectangles represent edges found in the graph. Above this rendering of the topology, the reference path from GRCh38 is shown (in green). Red and blue bars represent reads mapped to the graph. Thin lines in the reference path and read mappings highlight relative gaps (either insertions or deletions) against the full graph. The vg read mappings show consistent coverage even over the deletion. b Reads mapped to the linear genome reference GRCh38 using bwa mem [26] in the same region. Reads contain soft-clipped sequences and short insertions near the deletion breakpoints. Part of the deleted region is also covered by several reads, potentially confusing traditional SV genotypers