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 ?