CNV annotation tool

[clarissaboschi]

Dear all,

I detected CNVs with CNVnator tool from seq-data and after I identified the CNV regions with CNVruler. Now I need to annotate these regions.

Which tool I can use for it? I know that I can use bedtools or R (overlap), but is there any tool that I can use?

thanks

[lgmSeq]

AnnotSV: An integrated tool for Structural Variations (SV) annotation

I suggest using AnnotSV for SV/CNV annotation (with OMIM, DGV, 1000g, haploinsufficiency, TAD, ... and also with your own in-house information).

You can look at the following post describing the annotSV tool:

http://seqanswers.com/forums/showpost.php?p=218587&postcount=4