Problems wth cnvkit scatter for genes

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5.7 years ago

biologist ▴ 20

Hello,

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?

Thank you!

cnvkit • 1.6k views

ADD COMMENT • link updated 5.7 years ago by h.mon 35k • written 5.7 years ago by biologist ▴ 20

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

ADD REPLY • link 5.7 years ago by Nicola Casiraghi ▴ 500

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