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@tiagochst so shall we delete the negative values and 0 when calculating over survival? if do not delete it ,will it get a wrong conlusion thanks a lot?

I hope the author can give an "gif example" of using "cherry-pick"

but how it ensure the result is right, without the control. thanks a lot

because most tools need PoN or paired, thanks a lot.

https://academic.oup.com/bioinformatics/article/32/15/2375/1743834 

yes, you do not, what I want to say is that you compare canvas and cnvnator in germline calling, showing canvas better, but in somatic compare, you did not show...

On low purity or high ploidy purity samples, without performing purity/ploidy correction the CN calls will be incorrect. I do not understand this, is it convenient for you to clarify...

thanks for your clear examples, how do you think can get a better baseline for cnv, do you think a PoN(pool of normals) or a normal is better,

thanks for your professional reply, how do you think whether germline variants include some somatic variants is right? or somatic variants do not contains some germline variants. Sometimes somatic just...

canvas has five mode, is it ok to call cnv by just one tumor sample, without control or PoN, Somatic-Enrichment - CNV calling of a somatic sample from targeted sequencing...