Hi,
I am trying to run ichorCNA with the example files provided (MBC_315.ctDNA.reads.wig, MBC_315_T2.ctDNA.reads.wig). Are these the same samples explained in Figure 1.C in the manuscript (Adalsteinsson etal.,2017, Nature Communications)? Could you please give the tumor fraction estimate in these samples and the parameters used (for example: range of initializations for normal fraction (0:35; 0:45; 0:50; 0:65; 0:75; 0:85; 0:95) and tumor ploidy (2; 3; 4) anything else?) so as to replicate the output.
Thank you.
Hi, I am trying to run ichorCNA with the example files provided (MBC_315.ctDNA.reads.wig, MBC_315_T2.ctDNA.reads.wig). Are these the same samples explained in Figure 1.C in the manuscript (Adalsteinsson etal.,2017, Nature Communications)? Could you please give the tumor fraction estimate in these samples and the parameters used (for example: range of initializations for normal fraction (0:35; 0:45; 0:50; 0:65; 0:75; 0:85; 0:95) and tumor ploidy (2; 3; 4) anything else?) so as to replicate the output. Thank you.