The Output

What is produced

There will make two pairs Copy Number Profiles with different resolutions, one for the 100Kbp and 1000Kbp Bin size. And two reports, for each resolution, with the clonality result.

The Copy Number Profiles

Each sample has theirs profiles, one at 100Kbp and another at 1000Kbp. The profile is kind of a scatter plot, where each small black dot is a bin, the orange lines represent the "normalization" of a group of bins.
If the orange line is over the normalized log2 read count at 0, there might be a gain, if it is under, there might be a loss.

The Clonality report

As described, each sample pair will have a 100Kbp and 1000Kbp profile. The report is represented as 3 colours plane, a light yellow one that represent Non-clonal relation, light blue area for the Clonal ,and grey which is Inconclusive.