Hello. I'm new with pyclone and I'm trying to run a pyclone with WES data from TCGA. I need some information of allele specific copy number to make a input file for pyclone, but i don't know which tools I can use for it. I downloaded somatic mutation output of mutect file from TCGA and it has t_depth/t_ref_count/t_alt_count/n_depth, but there is no information about parental copy informaitons.
could you recommend any tools for find specific copy number data? And should I use the location only has 2 copies for pyclone?