CNV detection and annotation

tonio100680 · 10-29-2012, 08:55 AM

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, 09:49 AM

I think CNVnator is a good tool for it.

lgmSeq · 07-09-2018, 11:31 PM

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

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10-29-2012, 08:55 AM	#1
tonio100680 Member Location: FRANCE / Caen Join Date: Apr 2010 Posts: 25	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

07-09-2018, 11:31 PM	#3
lgmSeq Junior Member Location: France Join Date: Jun 2014 Posts: 5	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

05-13-2015, 09:49 AM	#2
clarissaboschi Member Location: US Join Date: Apr 2010 Posts: 63	I think CNVnator is a good tool for it.