Question: CNVPanelizer Package_Non reliable CNV
0
gravatar for Bouzid.a
8 months ago by
Bouzid.a0
Bouzid.a0 wrote:

Hello,

For CNV detection from targeted NGS data, I was running CNVPanelizer tutorial, I get an amplification as a non-reliable change in a gene of interest on my targeted gene list. Please, how can I further check this CNV, which tool/package you suggest to use in order to limit the region/interval of the resulted CNV knowing that CNVPanelizer allows classifying the copy number aberrations only on the gene level.

cnv cnvpanelizer • 179 views
ADD COMMENTlink written 8 months ago by Bouzid.a0

so, your goal is to find breakpoints of a CNV (if it exists)? it all depends on the parameters of your panel - how many genes are covered? is it ampliseq or hybridization-based enrichment?

ADD REPLYlink written 8 months ago by German.M.Demidov1.8k

Hi German, Exactly, that's what I 'm looking for. My gene panel is a hybridization-based enrichment of exons spanning 84 genes. Any recommendations, please?

ADD REPLYlink written 8 months ago by Bouzid.a0

I think the guys who wrote CNVPanelizers write from the first lines of their manual that it is designed for AmpliSeq enrichment panels. You may try ClinCNV, however the number of genes is not that big, so I am not sure if it will actually work...

ADD REPLYlink written 8 months ago by German.M.Demidov1.8k

Aaa it escapes me ! Thank you for your reply German.

ADD REPLYlink written 8 months ago by Bouzid.a0
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