Genotype information required in Clonality analysis using Pyclone

Question

[nilesh.gardi2688]

I have affymetrix SNP array data and exome data for same tumor samples. I want to run Pyclone for clonal evolution experiment. I identified somatic mutations in each tumor samples using varscan2. As per Pyclone requirement, I need to input these mutations along with parental copy number information. My question is to how to infer allele specific copy number from either exome sequencing or SNP array data? I need to populate major allele, minor allele and genotype information for each mutation. Kindy help.