Question: How is the "weight" calculated by CNVkit ?

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Hällyss •

**50**wrote:Hello,

We search a kind of score whilch can eliminates many FP call in CNVkit results. We think that the weight can be used. We search a signification of this weight, an equation. In the manual of CNVkit, we found this extract :

A weight is assigned to each remaining bin depending on:

- The size of the bin;
- The deviation of the bin’s log2 value in the reference from 0;
- The “spread” of the bin in the reference.

(The latter two only apply if at least one normal/control sample was used to build the reference.)

So, we have many questions :

- what "bin" means ? The segment ? The bin in my_target.bed ? my_antitarget.bed ?
- what is the "spread" ? the number of bins in the segment ? the length of the segment ? something else ?
- the score seems to be strongly affected by segment size and / or bin number in the segment, is this the case?
- is it possible to get an equation of the weight ?

Thank you

Alice

You wrote in the tags which tool this question is about, but that would have been useful information in your post as well.

43kAll of my apologies, thank you for your answer.

50