1 the cnvkit doc seems to be much later than the conda version, and there is not a good explatation of how to filter the final rersults depending on cn depth p_ttest probes weight
2 in the doc https://cnvkit.readthedocs.io/en/stable/pipeline.html?highlight=10x#reference, it mentioned "CNVkit will usually call larger CNAs reliably down to about 10x on-target coverage", so what is the recommended depth for tumor and normal samples, and the lowest depth
3 why the batch.py not including the parameter purity, I have read the code, in the line 201 abd 206,can I revise the code directly and add the parameter purity
4 if I have run the batch command, and I want to use the theta result, can I use the cns file for the export theta, I have tried thta, and it gives a pdf containing the tumot and normal percent, is thta the tumor purity, how can I get the value? and I use the theta, but it get more cna than just use the batch, what is the background reason?
5 how can I make my wes result more close to wgs result?
6 for small target panel, is there a limit of panel size for cnvkit?
thanks a lot
