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etal / cnvkit

Copy number variant detection from targeted DNA sequencing
http://cnvkit.readthedocs.org
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How to export segments #739

Open gtollefson opened 2 years ago

gtollefson commented 2 years ago

Hi,

I'd like to access the chromosomal coordinate and log2 data fields for all segments plotted in dark-orange in the scatter plot output from scatter.py. I noticed that the bins reported in the standard output files from the CNVKit batch command report all bins, not just the ones that are marked in orange as LOH/allelic imbalance. Is there any way to view the data for the segments that are plotted in orange in the scatter plots?

Thank you, George

tetedange13 commented 2 years ago

Hi @gtollefson,

If I understand your question correctly, maybe you should give a try to cnvkit.py export bed command ? => You could also manually filter your "cns" files produced, using awk for example (based on "CN" column of "log2")

Hope this helps ! Kind regards, Felix.