Question: Panel of tumors for CNV detection
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gravatar for biobiu
6 months ago by
biobiu110
United States
biobiu110 wrote:

Hi, I'm trying to detect somatic copy-number alterations in custom-targeted sequencing panel.

Most of the tools and methods published for this sake requires matched normal sample or panel of normals. However, we have no normal samples. We do have dozens of tumor samples sequenced with the same targets on with the same library prep methods, so, I believe we will be able to reduce the biases introduced by the target capturing and library preparation.

Did anyone tried to call somatic CNV with such "panel of tumors"? or familiar with tools that are less sensitive to this kind of setting? Best!

cnv panel of normals cna • 267 views
ADD COMMENTlink written 6 months ago by biobiu110

Following further reading- I think I'll try to use CNVkit, gatk and copywriteR. Did anyone tried these tools with such "panel of tumors"? or know which should be less sensitive for this kind of input?

ADD REPLYlink written 6 months ago by biobiu110
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