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
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.txtHowever 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