Inconsistencies between CNA and BAF files

[amcpherson]

From the following I would expect the copy number between 122701000 and 122702000 to be 0, since 122702000 is the end of the first segment for the predicted region on the 3rd line. In other words, the 3rd line represents a region from 122701000 to 135534000.

tumour.cna.subclone-2.txt

10 42027000  80660 122686000 0.000 0.000 0.000 1.000 0.000
10 122687000     15 122701000 0.000 0.000 0.000 1.000 0.000
10 122702000  12833 135534000 1.000 0.000 0.000 0.000 0.000
10 135535000      1 135535000 1.000 0.000 0.000 0.000 0.000

However from the BAF file, some SNPs within the 122701000-122702000 segment have copy numbers 1 or 2 which is incompatible with total copies 0.

tumour.baf.subclone-2.txt

10 122701679      2 122701957 0.080 0.420 0.420 0.080 0.000