In the CNV segment file, there is a status column including -, 0, + as status calls. I think they indicate copy number loss, neutral, and gain, respectively.
But when checking the range of SegmentMean (relative copy ratio) associated with each status, I got the following
in [0.5504624, 1064.008]
0 in [4.786971e-10, 19.22648]
in [4.903541e-11, 0.8999651]
The values of the three status calls actually overlap. So I am wondering about
(1) Do -, 0, + really mean copy number loss, neutral, and gain, respectively?
(2) How are the status calls generated based on the SegmentMean (relative copy ratio)?
Thanks for reaching out. DepMap currently uses the GATK somatic CNV workflow as our relative copy number caller. Please feel free to refer to their documentation here.
To answer your first question, the short answer is yes, but the cutoff has two layers (copy ratio cutoff AND z-score); and the explanation in this post might be helpful in answering your second question.
In addition, DepMap also has a step downstream of the GATK workflow where non-log2 copy ratios on chromosomes X and Y are divided by 2, which is reflected in the SegmentMean column, but their status is not changed. That also contributes to some of the overlap you are seeing.
