How to export segments

[gtollefson]

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]

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.

[etal]

Answered with export bed / awk filtering suggestion. Closing as answered — please reopen, or open a new issue, if a concrete problem remains.

For general usage questions, we now use GitHub Discussions (Q&A): https://github.com/etal/cnvkit/discussions