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  • cnv annotation

    Hi,
    I used ExomeCNV and FREEC on my tumor-normal matched exome sequencing samples to discover copy number variations. Now I need to combine and annotate the results.

    What kind of tools would you suggest for the task ?

    Can Annovar be used for annotation purpose of CNV files?

    Thanks


    Suleyman

  • #2
    • CNV/SV merging:
      To merge/combine the common CNV detected by your different callers, 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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