I have one question.
We wanted to call Copy number for some of TCGA WXS samples. But we noticed that the exome capture kit (target bed file) that was used, was based on hg18 (more specifically is was hg18 nimblegen exome version 2). In fact we went and verified that this bed file coordinates are actually from hg18.
Now from the bam file header it seems, it was mapped against GrCh37-lite which is a version of hg19.
So for most Exome CNV caller they need the capture target bed file as one of the inputs. But in this case it is not consistent with the reference genome version used in mapping. I think that'd be a problem.
So what would be the best way to call the copy number in this situation. Should we lift over the coordinate from the target bed file to GrCh37-lite ?