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tonio100680 10-29-2012 07:55 AM

CNV detection and annotation
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 05-13-2015 08:49 AM

I think CNVnator is a good tool for it.

lgmSeq 07-09-2018 10:31 PM

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:

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