Hi

I have a compiled segmentation file (nocnv) for almost 1000 samples. I want to calculate the copy number aberrations for all the samples.

I tried using GISTIC, but I believe it provides only the consensus copy number variations. Is there a better way to calculate copy number aberration from segmentation file.

Here are few lines from the segmentation file I have:

```
Sample    Chromosome    Start    End    Num_Probes    Segment_Mean
TCGA-E2-A1IH-01A-11D-A13J-01    1    3208470    42629316    20791    -0.2864
TCGA-E2-A1IH-01A-11D-A13J-01    1    42631290    42692913    60    0.0183
TCGA-E2-A1IH-01A-11D-A13J-01    1    42701180    42918495    113    0.3411
TCGA-E2-A1IH-01A-11D-A13J-01    1    42925163    43153569    131    -0.0548
TCGA-E2-A1IH-01A-11D-A13J-01    1    43153652    43599777    288    -0.3653
TCGA-E2-A1IH-01A-11D-A13J-01    1    43600151    44642193    575    -0.0401
```

Thanks

Meenakshi
You'll want to define some threshold for `|Segment_Mean| > X` because I would probably not consider all segments to be true copy number alterations. Filtering based upon length and number of probes is probably also a good idea.

I don't have a precise recommendation of what threshold to use, but I would try plotting density / histogram values for the Segment_Mean to guide your decisions.