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fritzsedlazeck / SURVIVOR

Toolset for SV simulation, comparison and filtering
MIT License
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Clarification on derivation of SV length and type #210

Open olivia-gc opened 4 months ago

olivia-gc commented 4 months ago

Hi, I am trying to understand how SURVIVOR filters and merges vcfs from different callers.

I just wanted to confirm that SURVIVOR tests multiple strategies to derive SV length depending on the type and caller. For ex: END - POS2 (instead of END - POS) for TRAs when SVLEN is not available.

I also wanted clarification on dealing with BNDs during merge. From my understanding, SURVIVOR will type BNDs to INV or TRA. With this, if I have vcfs for a sample that are separated by SV type, should I be merging INV vcfs from one caller with BND vcfs from another to see if there is a consensus call set between them?

Thank you very much for your help