CNV detection and annotation

[tonio100680]

Hi all,

I am currently looking for a software to determine CNV. Knowing that I am using data re-targeted sequencing (approximately twenty genes). CONTRA I could but I would know your opinion? What do you think is the best software to detect all types of CNV (deletion, duplication, inversion and translocation)?

Thank you in advance for your help

[clarissaboschi]

I think CNVnator is a good tool for it.

[lgmSeq]

CNV / SV detection and annotation

• CNV/SV detection:
  I suggest using different CNV callers: Control-freec, Lumpy, ERDS, BreakDancer
  I advise then to merge the common CNV detected by your different callers. For that, 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