2.2 years ago by
University College London
You just need the data in the format:
1 160283 471362 DUP
1 1385015 1387562 DEL
So, you need to set rules about copy number gain and loss based on the
segment_mean column in your data. I have seen values of -0.2 / +0.2 and -0.3 / +0.3 used, in the past.
If, instead, you are only interested in which genes overlap your regions right away, then take a look at my answer here: How to extract the list of genes from TCGA CNV data
Further down on that page ( C: How to extract the list of genes from TCGA CNV data ), I then actually go over how you can merge your copy number aberrations into recurrent somatic coy number alterations (recSCNA) and show how you can eventually end up with regions as AMP (DUP) or DEL, which is suitable then for VEP.