Plot copy number integer with segment

Open jnaccara opened this issue 3 years ago • 2 comments

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.

Jan 10 '22 21:01 jnaccara

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.

Jan 19 '22 02:01 ouslalu

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

Feb 22 '22 05:02 etal