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etal / cnvkit

Copy number variant detection from targeted DNA sequencing
http://cnvkit.readthedocs.org
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Plot copy number integer with segment #682

Open jnaccara opened 2 years ago

jnaccara commented 2 years ago

Is there a way to display copy number integer when using cnvkit.py scatter? I just started using cnvkit this week and cannot find the option. Ideally, the copy number integr would be displayed on the segment in the scatterplot.

ouslalu commented 2 years ago

The .cns file from which the scatter diagram is plotted does not have the copy number integer information. You might want to check the .call.cns file.

etal commented 2 years ago

No, it's not an option yet. CNVkit needs another step to estimate integer copy numbers; initially it only estimates read depth log2-ratios. https://cnvkit.readthedocs.io/en/stable/calling.html