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Tool for structural variation detection of plant WGS data

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.

plants structural-variation wgs
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written by Bushra Bibi Bushra Bibi

1 answer

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.

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written by dthorbur dthorbur

So kind of you dthorbur. Many thanks!

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written by Bushra Bibi Bushra Bibi

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