The Broad Institute did the CNV analysis for the TCGA samples. The only information I have been able to find about the reference genome* does not give the version of hg19 they are using. I have two questions:
- Is hg19 exactly the same as Ensembl's GRCh37?
- It looks from the Ensembl site that the data has had various patches and updates. I have a list of CNV start end co-ordinates and want to extract the genes involved. How much difference will it make if I use a version with the wrong patches?