cnv annotation

[svural]

Hi,
I used ExomeCNV and FREEC on my tumor-normal matched exome sequencing samples to discover copy number variations. Now I need to combine and annotate the results.

What kind of tools would you suggest for the task ?

Can Annovar be used for annotation purpose of CNV files?

Thanks


Suleyman

[lgmSeq]

• CNV/SV merging:
  To merge/combine the common CNV detected by your different callers, I would consider CNV that share a 70% reciprocal overlap measured by length and position (> 70% shared length) (as done in DGV).
  
  
• CNV/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/showpos...87&postcount=4