CNV analysis genes

Question

[alromisashamoon]

I have analyzed cnv cell files of affymetrix using Genotype Console. But I can't seem to my result in a form of genes that have been duplicated or trimmed. is there any free software or tool can do such a thing. annotating my result in to genes. I know that R software can do what I am asking for .but I don't know who to use it.

Thanks for your time.

Answer 1

[Emily]

You can use the Ensembl VEP for this. There's full documentation on using both the online tool or the Perl script (already written - no Perl-ing on your part - just plug in the commands) to analyse structural variants. It'll give you a list of all the genes that have been ablated/amplified, plus those that have been cut in two.