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etal / cnvkit

Copy number variant detection from targeted DNA sequencing
http://cnvkit.readthedocs.org
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CNVkit exon del detection #654

Closed skose82 closed 2 years ago

skose82 commented 3 years ago

Hi all,

I've produced two scatter plots from two different samples. I am looking for an exon 2 deletion in the SUFU gene in sample 2. I produced a scatter plot of sample 1 as a control as this sample does not have any known exon 2 deletions. The output of the plots are quite different.

  1. Is there a way to zoom in on chr10 to the SUFU exon 2 region to see if a deletion is present in sample 2?
  2. Why are these plots so different in general? e.g. why is the orange baseline slightly lower in sample 2?
  3. Is there a better plot to use than scatter?

Any advice would be greatly appreciated.

Best wishes sample1_scatter sample2_scatter

enes-ak commented 3 years ago

Hi, I am not an author of cnvkit but I have some experience with this tool.

you can use that code if you know the exact location of your interested exon cnvkit.py scatter -s Sample.cn{s,r} -c chr10:start_loc-end_loc

or you can use that code cnvkit.py scatter -s Sample.cn{s,r} -c chr10 -g SUFU

Are you sure about the select true bed file for analysis? target regions and your experiment bed file should be the same to take reliable results.

skose82 commented 2 years ago

Thanks enes-ak, I ended up using a different program in the end which was a little more straightforward.