Any suggestions for changing the default parameters in ichorCNA for tumour tissue? I have successfully run ichorCNA for tumour samples but for male samples (as characterized in params.txt file) the Chr Y is always empty in plots, no points. I am using default parameters. Any idea on how to get that.
I am using my own panel of normals and have included Chr X and Chr Y in that.
Hi Gavin,
Any suggestions for changing the default parameters in ichorCNA for tumour tissue? I have successfully run ichorCNA for tumour samples but for male samples (as characterized in params.txt file) the Chr Y is always empty in plots, no points. I am using default parameters. Any idea on how to get that.
I am using my own panel of normals and have included Chr X and Chr Y in that.
Thanks