Fig. 2

Matching SVs for Annotation Creation. a SVAFotate expects two distinct input files: an unannotated SV VCF file and a BED file which may contain SV calls from multiple population datasets and their accompanying AF metrics. To represent the SV calls in these files, unannotated SVs are illustrated as gray rectangles while SVs from three different datasets, such as CCDG, gnomAD, and 1000G, are represented by green rectangles with their reported population AF included as labels. For this example we will assume that all rectangles represent SVs of the same SVTYPE. SVAFotate attempts to identify matches between unannotated SVs and the SVs present in the BED file by identifying genomic coordinate overlaps that meet user-defined criteria between SVs of the same SVTYPE. Multiple matches are possible, and all AF related data is saved for each match. b SVAFotate is capable of generating multiple annotations that are added to the original VCF file and are each derived using information saved from matching the SVs. The types and variety of annotations added to the VCF are determined by input parameters provided at the command line, but here the example annotation added is the Max_AF (default) annotation