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etal / cnvkit

Copy number variant detection from targeted DNA sequencing
http://cnvkit.readthedocs.org
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Interpreting the results #921

Open MaryGoAround opened 1 month ago

MaryGoAround commented 1 month ago

Hi

For WGS with no control, from which part of the results I can say if there is a duplication in a certain chromosome?

Thanks a lot

etal commented 1 week ago

Generally it's safe to say that if the .call.cns file shows a copy number of 3 or more for the chromosome, or the log2 ratio in the .cns is around .58 or higher. The chromosome might be covered by a single segment, or if the signal is noisy then you might see some spurious breakpoints while the rest of the chromosome is fairly consistently showing an elevated log2 value. The .call.cns file is usually the better source for making this determination.