SoftSV

SoftSV is a tool for the detection of small and large deletions, inversions, tandem duplications and translocations from paired-end sequencing data. It uses aberrant paired-end mappings to determine approximative breakpoint regions and refines the breakpoints by analysing soft-clipped sequences for potential split-reads.

For more information about the algorithm and an evaluation, have a look at this publication:

"Robust and exact structural variation detection with paired-end and soft-clipped alignments: SoftSV compared with eight algorithms"
(PMID 25998133)

Please cite this artilce if you used SoftSV in your publication.