Given two genome .bam files, one of which we know is from a tumor sample and the other from normal/germline from the same person, is there an efficient way to correctly identify them bioinformatically?
A simple approach is to use a copy-number or allelic imbalance analysis. Such analyses will almost always show significant abnormalities in the tumor sample. While there will also be copy number and apparent blocks of loss of heterozygosity in a "normal" genome, tumors typically have this to a much larger extent. There are many tools to do copy number analysis; the particular choice will probably not make much difference for such a broad question.