I'm trying to get input file for THetA 2 using CreateExomeInput command. I'm giving the segment file for this command as the Varscan 2 output file after CBS segmentation with these columns
chr loc.start loc.end num.mark seg.mean chr1 69268 12327976 1055 1.6745 chr1 12327999 12395859 112 1.33 chr1 12395959 12398149 3 -1.0807 chr1 12398177 12836275 167 1.3756
However, in the output I get 0 for both tumor count and normal count. I'm using hg19.fa & for the exon file I'm using hg19.exons.bed file as given in the THetA folder. Can someone please help if the output is 0 due to my input data or is there anything I can do to solve it.