Hi, I want to use sciclone on our exome sequencing data. but one thing I can't understand that is how can I got varCount equal to 0? I have no idea about this,
following data i just grep from sciclone-meta-master manuscript figure3 data vaf input:
so if that is the case, I totally wrong? I used GATK merged vcf, and use R (data.table) to manipulate and got final input files.
I just wonder if anyone can help me and give me some advice. and would you mind to teach me how to calulate (vcf ./.) the depths for those paired samples only one sample have mutaiton but other one no mutation? bedtools coverage? or other ways?
I have one more question for building clonal evolution, since when I use sciclone to calulate subclone, I already remove those un-neutral region, after got subclone info, can I add those CNV changed region back to build evolution event? I ran THetA2 succesfully, I plan use sciclone + THetA2 to test the evolution. plot by fishplot. Thanks. Haitao