Best Discordant Pair Structural Variant (Sv) Caller?

Question

[William]

What is the best discordant pair structural variant caller at the moment?

The most popular one used to be BreakDancer. But that is lacking VCF output I think and is based on my knowledge from a couple of months ago.

I think some new discordant pair callers have been released the last couple of months but I didn't check them out yet.

Is BreakDancer still the go to discordant pair SV caller or are there other good / better options for discordant pair SV calling? A caller with a nice VCF output is preferred to make downstream processing easier.

[Ashutosh Pandey]

I have tried BreakDancer and GASV, GASVPro. Both worked good for me.

[richard.deborja]

I've been following the DREAM SV detection competition. I've been using Delly since it does both split read and discordant pairs. It takes quite a long time to run in somatic mode but I have been pretty happy with the results. Recently I tried Manta and am still attempting to interpret the output but so far the results seem accurate although I worry it may be undercalling variants.

[Malachi Griffith]

The OMIC tools website has a decent list of SV tools.

Answer 1

[Malachi Griffith]

More options:

• GASV and GASVpro (paper)
• lumpy-sv (paper)
• CREST (paper)
• HYDRA (paper)
• Meerkat (paper)
• Manta (pre-print, paper in preparation)
• delly (paper)
• Pindel (paper)
• NovoBreak (paper?)
• destruct
• svdetect
• PeSV-Fisher (paper)

Answer 2

[Rm]

some more SV tools (Not VCF output though)... SVDetect, DELLY, PeSV-Fisher