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Old 01-14-2014, 03:47 PM   #1
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Default cnv annotation

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?


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Old 07-09-2018, 11:37 PM   #2
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  • 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:
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cnv annotation

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