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How Can I Annotate Cnvs

Hello,

I have human paired end Illumina genome data. I wish to analyse the CNVs. I used FREEC software to detect the CNV and now I have an output which looks like this

1       1280000      1290000      6       gain
1       1280000      1290000      6       gain   
2       53570000     53580000     4       gain    
4       190470000    190680000    7       gain   
5       5230000      5370000      3       gain

How can I analyse the CNVs further ? Is there any way I can annotate these CNVs ?

Thank you.

cnv
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updated by Min • Min • written by NB NB

what do you want to annotate them with?

• 0 views • link
written by brentp brentp

mainly the genes affected and its function

• 0 views • link
written by NB NB

I suggest using AnnotSV for CNV annotation (with OMIM, DGV, 1000g, haploinsufficiency, TAD, ... and also with your own in-house information) .

You can look at this post describing the annotSV tool: Annotation for SV and CNV

• 1 views • link
written by LGMgeo LGMgeo

3 answers

What do you want to know about them? If you'd like to know what genes they affect, you could try to Ensembl VEP. You'll need to convert them into VCF format though.

http://www.ensembl.org/info/docs/variation/vep/index.html

• 120 views • link
written by Emily Emily

ANNOVAR is capable of annotating CNVs

• 36 views • link
written by Robert Sicko Robert Sicko

Please try http://bioinfo.mc.vanderbilt.edu/CNVannotator/

• 40 views • link
written by Min • Min

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