Fig. 5

Recommended SVAFotate Parameters. Each plot illustrates SVs from the input VCF as gray rectangles with colored rectangles representing SVs from various datasets, such as CCDG, gnomAD, or 1000G. In all examples, the SVs depicted by gray and green rectangles are of the same SVTYPE. a Requiring a reciprocal overlap with the -f parameter specifies that SVs being compared to one another must each have an overlap that meets a minimum fraction of the total size of the SV in order to be counted as a match and saved for future annotations by SVAFotate. On the top, the -f parameter is not being used and any overlap, regardless of size, is being counted as a match, while on the bottom, -f is being used with a value of 0.8 which reduces the number of matches to those with greater overlap similarity. b The OFPs for potential matches are calculated and listed as labels on each of the colored rectangles, representing SVs from three different datasets. The “best” match is determined by the match with the highest OFP value and metrics specific to that best match are saved and used for subsequent SVAFotate best annotations. If no match exists as illustrated for the SV on the left for Dataset 3, no best annotations are added for that dataset. c Gray rectangles represent deletions from the input VCF and colored rectangles represent different SVTYPEs, specifically deletions (red), duplications (blue), and inversions (purple). Matches are defined as SVs of the same SVTYPE that overlap one another while mismatches are SVs of differing SVTYPEs that share an overlap. d For each SV from the input VCF, all overlaps are saved and used to determine how much of the total SV region has also been observed in the datasets which is then reported as the SV_Cov annotation.