svWGS
The svWGS pipeline and app analyze paired-end, short-read whole genome sequencing (WGS) data to find individual high-confidence SV junctions.
A premium is placed on building a comprehensive evidence base to support individual junction calls as being real above the ever-present baseline SV artifact levels. This might include either clonal or mosaic SVs with multi-molecule evidence, or ultra-rare mosaic molecules only expected to be found once in the input library.
While the focus is on careful characterization of junctions, the pipeline and app also monitor copy number status to support clonal deletion and duplication junctions by parallel CNV assessments.
svWGS is not as useful for finding stretches of DNA containing multiple SVs and characterizing their paths - the reads are too short for this (see svPore). It is also not generally intended to produce a final comprehensive “true call set” of all SVs in a sample, although one can be produced after applying some desired set of quality filters to the complete table of all possible SV junctions.