Best Discordant Pair Structural Variant (Sv) Caller?
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7.7 years ago
William ★ 4.8k

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.

vcf sv discordant variant caller • 7.5k views
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I have tried BreakDancer and GASV, GASVPro. Both worked good for me.

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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.

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

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7.7 years ago
Rm 8.0k

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

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