The ‘relative CN’ is the Segment_Mean from the segment file that covers the gene (padded and averaged across the coordinates). For the cell line you’re pointing to (ACH-000219) ENO4 is covered by the following segment in the segment file:
DepMap_ID Chromosome Start End Num_Probes Segment_Mean Source
ACH-000219 10 77116708 133797422 3634 1.060220 Sanger WES
The copy number value is log2(1.060220+1) = 1.04
To get the Segment_Mean we calculate 2^MEAN_LOG2_COPY_RATIO, where MEAN_LOG2_COPY_RATIO is the output from GATK4. MEAN_LOG2_COPY_RATIO is not exactly the log-transformed ‘relative CN to ploidy’ but rather the result of GATK4 tool which includes PoN correction through SVD and median adjustment plus a shift to 1.
The absolute copy numbers are from ABSOLUTE package. The inconsistency between the relative and absolute numbers can be due to incorrect inferences done by either/both algorithms.
