a) I don't know of any off-the shelf tools, b) this is generally difficult, because breakpoint-spanning reads may map to one side or the other, but also may not map at all. To get a high confidence call, you could create a short contig containing your breakpoint sequence +/- 200 bp, append it to the reference genome, then realign all of your reads against this. Compare the depth of breakpoint spanning reads on your contig to the depth at the breaks on the original reference sequence, and that ratio will give you a pretty good idea of the frequency. - Chris Miller