Question: Weights in cnvkit cnr output
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gravatar for biologist
9 weeks ago by
biologist10
biologist10 wrote:

Hello everyone,

I have tried reading up on different biostars posts about cnvkit's cnr column weights but am still confused. From https://cnvkit.readthedocs.io/en/stable/pipeline.html, I understand that weights in .cnr are dependent on the size of the bin, deviation of the bin’s log2 value in the reference from 0 and spread” of the bin in the reference. I am not particularly familiar with these terms and so could someone explain what exactly this means and if I can take the cnr's weight column as a measure of how confident we can be about that particular CNV call?

Also, if I want to look at a particular range of a chromosome to look for a CNV that is made up of 5 rows from the cnr output for example, do I take the average value for the 5 log2 values but the SUM of the 5 weight values? I am asking because How is the "weight" calculated by CNVkit ? says that cns takes the sum of the weights of all the bins that make up that segment. In this case, would a higher weight be equivalent to a more confident call?

Any advice is appreciated, thanks!

cnvkit • 116 views
ADD COMMENTlink modified 1 day ago by Biostar ♦♦ 20 • written 9 weeks ago by biologist10
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