Any techniques faster than Breakdancer?

Question

[boyu93]

I have been using Breakdancer for structural variant detection, but it is running so slow, which takes more than 30 hours for a pair of tumor/normal samples as to WGS data. Are there any other methods which can do similar stuff but run faster? Thanks,

[boyu93]

That's what I want to find in this link, a compile of SV caller packages. Thanks a lot natasha.

Answer 1

[Eric T.]

Yes: try LUMPY or Manta.