CNVkit plotting tumor + healthy individuals

Question

[bitpir]

Hi, I was just wondering if there's any way to plot a heatmap of all affected/tumor samples + the normal samples together? I think the default is set to plot the affected samples only.. Thanks!

Answer 1

[Eric T.]

Sorry I missed this. The heatmap command will plot any .cns or .cnr files you give it, so to show normal samples, give it the normal samples' .cns or .cnr files. If those don't exist yet (e.g. via batch), you can create them using the fix and segment commands.