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Old 10-29-2012, 07:55 AM   #1
tonio100680
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Location: FRANCE / Caen

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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
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Old 05-13-2015, 08:49 AM   #2
clarissaboschi
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I think CNVnator is a good tool for it.
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Old 07-09-2018, 10:31 PM   #3
lgmSeq
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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:
    http://seqanswers.com/forums/showpos...87&postcount=4
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