Currently, I'm researching to get the minor, major copy number in tumor samples, so that I can use them in Pyclone. I have tried CNV caller such as PureCN, Sequenza and TitanCNA so far.

The caller calculates the most optimal ploidy, purity combination through likelihood and the result of one of my tumor sample was purity =0.7, ploidy = 5.254.

When I try to interpret the result, I keep on facing a problem. I believe that 'copy number log ratio' = 0 means that the normalized normal sample's depth and the normalized tumor sample's depth are equal and since ploidy of normal sample are diploid, the copy number that indicates 'copy number log ratio'=0 must be 2.

However, the result with the most optimal combination, the copy number log ratio' = 0 points toward integer other than 2. For instance 5 for the case I talked above.

Am I misunderstanding something? Should I have to pick an alternative solution or it is okay to go with the current optimal result?

I would really appreciate any replies because currently I am stuck.... and surely need some help

From Jenny

Just an hypothesis: could it be that the graph is plotting the log2ratio of the tumor ploidy in each position vs the average tumor ploidy? In that case you would expect 0 when the copy number is 5.24 (i.e. the tumor ploidy). Knowing the exact software and command that generated the plot could help.

Thank you for the quick reply. I quickly looked up the explanation for the plot and it states " tumor vs. normal copy number log2-ratios for the maximum likelihood solution".