Hi GATK Team,
When I use the GATK CNV workflow. I notice in the output file *.igv.seg, the `Segment_Mean` is centered at 1. In your documents, I found "The mean log2 copy ratio is given in the SEGMENT_MEAN column." In my results, this column is 0-Inf, and it doesn't feel like a log2 number (no negative). I feel it is more like a raw number of coverage sample/ coverage PON and take the mean in the region. So I would like to ask:
1. Where does the `log2` take place in segment mean calculation?
2. How and why does the program center the segment mean at 1? I see other tools center the log2 copy ratio at 0 which makes sense to me (log2(2/2) = 0 ).
3. I noticed the `MEAN_LOG2_COPY_RATIO` in `*.called.seg` files are very similar to log2(Segment_Mean) but slightly different. Is there any calibration in the transformation?
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