Question: Panel of tumors for CNV detection
gravatar for biobiu
7 weeks ago by
United States
biobiu90 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 • 119 views
ADD COMMENTlink written 7 weeks ago by biobiu90

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 7 weeks ago by biobiu90
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1515 users visited in the last hour