I was using CNV kit for Whole Exome Sequencing data (male samples) ploidy visualization.
The first time CNVkit was run without the -y option; which gave me a scatter figure that showed all autosomes to have a copy number ratio of 0. However, the X chromosome copy number ratio was -1 and 0 for chromosome Y. At the second trial the -y option for male reference was added which gave me a different result which showed a copy number ratio of 0 for both X and Y.
These results raised me 2 questions:
For autosomes, the normal copy number ratio would be log2(2/2) = 0 Is it normal for the X chromosome without the -y option to end up in log2(1/2) = -1 ? ; because chromosome X showed 0 for copy number ratio when the -y option was on. Is there a compensation algorithm for males because they have only one X chromosome?
And if the Y chromosome copy number ratio is 0, does it mean the sample is XYY or is there another algorithm that compensates the Y chromosome copy number ratio as it appears only in single doses in normal males which should look like log2(1/2) = -1 in normal male samples? (It showed 0 for both cases, with and w/o the -y option).