Question: Panel of tumors for CNV detection
gravatar for biobiu
20 months ago by
United States
biobiu120 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 • 610 views
ADD COMMENTlink modified 7 months ago by lffu_003260 • written 20 months ago by biobiu120

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 20 months ago by biobiu120
gravatar for lffu_0032
7 months ago by
lffu_003260 wrote:

In order to call CNV using catpure daga, you must need the normal or panel or normal data. the tumor data is so complex for its purity and ploidy, so the tumor data is not suit for being the control.

ADD COMMENTlink written 7 months ago by lffu_003260
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