We have 95 pairs of samples (tumor v.s. normal) that are whole exome sequenced. We identified 5 tumor samples do not have matching normal samples, and there are sample swapping happened.
Can we still use 5 tumor samples assuming that the 5 tumor samples are correctly labeled, but matching normal samples are wrong? Can we use the data from 90 normal samples and get panel of normal and try to identify somatic mutations for the 5 tumor samples based on the panel of normal? If this is possible, how I should proceed?