My data is two samples: tumor and normal ,exome and whole genome sequencing data.
I have tried XHMM for CNV analysis，but it needs more than 2 samples，so I changed to CNVnator and CNVFinder，but they are very hard to install in my system since I do not have root access and centos needs many other libraies which are not installed in my system.
I used CNVseq too，but the outcome is not very good.
I used varscan2 to analyze CNV，but the outcome is not very good either.
So is there any other CNVtools for tumor-normal sample ?