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etal / cnvkit

Copy number variant detection from targeted DNA sequencing
http://cnvkit.readthedocs.org
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Gain and Loss for WGS #518

Open anupullanhi opened 4 years ago

anupullanhi commented 4 years ago

Hello, I am working on CNV calling for the WGS sample. I generated .cnr and .cns files using batch and --method wgs option.

When ideogram was generated using diagram option, it was a very clumsy file. I would like to know how the calculation for gain and loss is done while generating the ideogram. Below given is the script I used to generate ideogram:

cnvkit.py diagram -s sample.cns -t 0.4 -m 5 -y -o sample_cns.pdf

I also generated a TEXT file using genemetrics option using the below-given command:

cnvkit.py genemetrics -s sample.cns -t 0.4 -m 5 -y -o genemetrics.txt

Could you offer recommendations to generate a customized ideogram diagram for CNVs called?

Thank you very much in advance!!

etal commented 4 years ago

The ideogram does not behave well for WGS samples since there tends to be too much information to show on one plot. You can try the --min-probes option to limit the display to larger alterations, or you can try filtering the segments in the .cns file with segmetrics and call to limit the display to higher-confidence calls. Finally, if you want to show only a specific selection of alterations you can edit the .cns file however you like to retain just the rows you want to display, e.g. genes of interest.

anupullanhi commented 4 years ago

Dear Etal

Thank you for your response.

I would like to know what is the threshold used for calculating gain and loss while generating ideogram for WGS. Any help regarding this is appreciated.

Thanks in advance

JD12138 commented 1 year ago

Dear Etal

Thank you for your response.

I would like to know what is the threshold used for calculating gain and loss while generating ideogram for WGS. Any help regarding this is appreciated.

Thanks in advance

I have the same question.