Dear all, please may I ask for your opinion :

when analyzing the somatic Copy Number Alterations (CNA) in the cancer genomes (based on whole genome sequencing data), would you recommend using (running) the CNA_calling algorithm :

-- per EACH CHROMOSOME individually, or

-- on ALL CHROMOSOMES at the same time (on a genome-wide scale) ?

I am asking because multiple copies of a chromosome may potentially introduce biases when computing the baseline corresponding to the diploid status of the genome. Thank you !

-- bogdan