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  • 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

  • #2
    I think CNVnator is a good tool for it.

    Comment


    • #3
      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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