I a newbie in bioinformatics. I am now analyzing whole exome sequencing data, and the samples are normal tumor matched. I am currently using varScan2 to do CNV calling. The input of varscan need a matched normal and tumor data, however, because we are worried about the purity of the normal sample, we want to use pooled normal data instead to compare with each tumor data. Not sure if I can do in this way.
I know varscan2 can do variant calling use pooled data, does pooled normal also works for CNV calling?
Thanks a lot in advance, Peng