I have a .cnr and .cns file from cnvkit after running it on a tumor-germline paired sample. I would like to plot genes to see the cnvs per exon if possible and so I am using the cnr file to do this.
These are some of my rows from the .cnr file for PTEN:
chromosome start end gene depth log2 weight 10 89623940 89624205 PTEN 29.224 -1.813344 0.600123 10 89624205 89624470 PTEN 149.901 -0.78201 0.750174
My command is :
cnvkit.py scatter -s Tumor.cnr -g PTEN -o pten.pdf
This graph I get has no points and has a block highlighted as PTEN. Could anyone suggest why I am not able to see the points under PTEN?
Is there a way to plot exons on this plot as well so that I can figure out what exons have undergone a CNV change?