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cancerit / ascatNgs

Somatic copy number analysis using WGS paired end wholegenome sequencing
http://cancerit.github.io/ascatNgs/
GNU Affero General Public License v3.0
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Copy number changes of ploidy-gain sample #95

Closed wanhui5867 closed 4 years ago

wanhui5867 commented 4 years ago

Hi,

I have several tumor samples that had a ploidy gain (2n -> 4n) comparing to the normal sample. When plotting the Copy number changes, all chromosomes of those tumor samples show color change. (please see below figure: bottom is copy number of each sample (darkgreen-green-grey-orange-red presents copy number from 0-1-2-3-…) image

However, it is strange that all chromosomes have a copy number gain in the tumor cell. Do you have any suggestions about presenting the copy number change of ploidy-gain samples?

keiranmraine commented 4 years ago

I recommend you raise this question with the developers of the underlying R package. We only provide support for the ngs wrapping code and easy execution:

https://github.com/Crick-CancerGenomics/ascat

wanhui5867 commented 4 years ago

Thanks for your advice!

I moved my question to the ASCAT R package: https://github.com/Crick-CancerGenomics/ascat/issues/61