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Old 10-29-2012, 08:55 AM   #1
Location: FRANCE / Caen

Join Date: Apr 2010
Posts: 25
Default 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
tonio100680 is offline   Reply With Quote
Old 05-13-2015, 09:49 AM   #2
Location: US

Join Date: Apr 2010
Posts: 63

I think CNVnator is a good tool for it.
clarissaboschi is offline   Reply With Quote
Old 07-09-2018, 11:31 PM   #3
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Location: France

Join Date: Jun 2014
Posts: 5
Default 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:
lgmSeq is offline   Reply With Quote

annotation, cnv, detection, software

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