Question: Problems wth cnvkit scatter for genes
gravatar for biologist
11 weeks ago by
biologist10 wrote:


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 : 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?

Thank you!

cnvkit • 203 views
ADD COMMENTlink modified 11 weeks ago by h.mon26k • written 11 weeks ago by biologist10

You can export the whole .cnr file as SEG tab-delimeted format and visualize it on IGV

ADD REPLYlink written 11 weeks ago by Nicola Casiraghi450
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