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etal / cnvkit

Copy number variant detection from targeted DNA sequencing
http://cnvkit.readthedocs.org
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How to normalise different sequencing coverage samples in CNVKit? #824

Open tanbiswas opened 1 year ago

tanbiswas commented 1 year ago

Hi I'm using CNVKit to identify copy number alterations using WES data. However, our tumor samples have a coverage of 200x and corresponding normal samples have a coverage of 100x. So, is there a way to normalize the coverage before calling CNV using CNVKit?

Please let me know hoe to proceed.

bahreinia commented 7 months ago

Hi, I am having the same question. We are using a panel of normal samples with 100x coverage as the reference for each tumor sample with a coverage of 300x. I would appreciate if someone could help. Thanks