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:
refCount varCount 261 0 102 0 1462 0
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?
Thanks so much, Haitao