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Old 07-09-2018, 10:31 PM   #3
lgmSeq
Junior Member
 
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:
    http://seqanswers.com/forums/showpos...87&postcount=4
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