Tool for structural variation detection of plant WGS data

Question

[analyst]

Dear all, I have been calling SNPs and indels from WGS data but I have never performed structural variation calling. Please suggest any tool to identify structural variations from plants WGS data. Does freebayes facilitate this?

Looking for your valuable suggestions.

Thank you.

Answer 1

[dthorbur]

There are so many tools available and a variety of underlying methodologies depending on data availability. Personally, I like LUMPY and DELLY2, and then make a consensus among calls using SURVIVOR.

However, this was a few years ago and I'm sure the field has moved on a bit. A quick literature search found 2 comprehensive papers benchmarking tools here and here.

[analyst]

So kind of you dthorbur. Many thanks!