I'm trying to search CNV on patients with my somatic panel (15 genes) and I'm interesting about CNVkit.
The first steps are to creating target and antitarget bed. And I have few questions about it :
1- In the manual : " CNVkit uses a cautious default off-target bin size that, in our experience, will typically include more reads than the average on-target bin." I don't understand, the mean of RC in the off-target must be higher than the mean of RC in the in-target or the total of RC in the off-target must be higher than the mean of RC in the in-target ?
2- I think it's the first probability, so i create a antitarget bed whilch the mean RC is equal to the mean RC of in-target. The split of my_target.bed is 100 (like your recommandation for deep sequencing) and for my_antitarget.bed is 1 200 000. Is there a problem if the segments of target and antitarget have not the same length (x 12 000 is maybe too big ?)
3- In the antitarget we have lots of part with 1X or 0X for the depth of coverage (maybe 80-90% of the antitarget). Is it a problem ? Does CNVkit make differencies between antitarget with coverage and antitarget without coverage or specificity ?
thank you for your answer and sorry for my bad english