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etal / cnvkit

Copy number variant detection from targeted DNA sequencing
http://cnvkit.readthedocs.org
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Script for cn_ztest.py not available. Posted on Biostars #649

Closed skose82 closed 2 years ago

skose82 commented 3 years ago

Posted by Eric T. However, link is no longer working. Is there another way to plot log2 scores? https://www.biostars.org/p/272590/

tetedange13 commented 3 years ago

Hi @SKose9 ,

Not an author of CNVkit, but since latest version, cnv_ztest.py script were replaced by a dedicated subcommand cnvkit.py bintest (see this release note) => Some bugs were fixed too, so please update to latest version => We are working to add this to CNVkit documentation soon

Hope this helps. Have a nice day. Felix.

skose82 commented 3 years ago

Thank you for your response. It was most helpful. In addition, Is there a way to see the bintest result in a plot of some sort? I'm trying to detect exon deletions in particular. I would like to zoom in on a chromosome to visually see if, say, an exon has been deleted in a particular region/gene, currently I can produce a scatter plot that displays everything (chr1-chrM). I can't quite see where to do this in the manual/docs. sample1_scatter