I have been using BreakSeq for identification of SV along with Break Dancer, CNVnator and Pindel. I was able to run BreakSeq and get SV. However, recently while submitting data to dbVar, I came know that I should also provide information on SIZE of SV. As BreakSeq output does not mention SIZE of each SV’s in its output it has become bit difficult to provide SIZE information to dbVar. However, I find POS and END position in output. Can I consider difference of POS and END as SIZE of SV?
For deletions you can use the pos and end for size. For insertions, the current version does not give you the size. We are planning for a next version which should have size. If you have to get it now, you can basically get the size from the insertion fasta distributed along with breakseq.