Hi.
I will ask a simple question regarding annotation method.
Firstly, I have found many structural rearrangement using DELLY, CREST and SVDetect.
Among many types of structural variants, I want to focus on structural rearrangement such as Inversion, Large deletion and translocation.(not SNPs, or Indels).
To know whether these rearrangement variants were reported previously and to find out more significant variants among them, I used annotation tool (Annovar) and I found that region-based and filter-based methods will fit for my purpose. Therefore, all my structural variants were annotated by gene based firstly and subsequently I used region-based and filter-based to find out more important variants.
But there is nothing variations reported passing through the region-based filter. I guess that Annovar especially is specialized in SNPs or small indes not rearrangement variation, so there are no reports for rearrangement variations. ( I can hardly find any results from filter based. not gene based.)
So Is there any suitable or appropriate annotation tool for structural rearrangement?
It seems that annovar doesn't fit for rearrangement.
Check out this tool for annotation of translocations/deletions and inversions that result in gene fusions Oncofuse: Prediction Of Driver Gene Fusions From Ngs Data. As for deletions/amplifications, I believe that the general working strategy would be to identify the list of affected genes (this could be simply done by .bed intersection in Galaxy) and using open annotation services, such as DAVID for those genes.
I suggest using AnnotSV for SV annotation (with OMIM, DGV, 1000g, haploinsufficiency, TAD, ... and also with your own in-house information)
You can look at this post describing the annotSV tool: Annotation for SV and CNV