CNVKit - Gene labels in 'diagram'

Question

[asjannu]

Hi, I have used CNVkit.py on targeted sequencing, did the segmentation and called the segments. Using -diagram option,I plotted ideograms for my files. My only concern is I couldn't get how I can set a threshold such that only significant genes appear on the ideogram. I know that 'diagram' option considers a threshold of 0.5. But, I would like to make my diagram look more stringent and have the most significant genes labelled.

Answer 1

[Eric T.]

I've documented some suggestions for dealing with this problem here: http://cnvkit.readthedocs.io/en/latest/plots.html#reducing-cluttered-gene-labels