How Can I Annotate Cnvs

Question

[NB]

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.

[brentp]

what do you want to annotate them with?

[NB]

mainly the genes affected and its function

[LGMgeo]

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

Answer 1

[Emily]

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

Answer 2

[Robert Sicko]

ANNOVAR is capable of annotating CNVs

Answer 3

[Min]

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