I have WES for 6 tumors which do not have matching normals. I identified all mutations, both germline and somatic with GATK. Then excluded all mutations that are considered as germline by ExAC, and germline mutations that are identified from our about 90 normal samples. The number of somatic mutations identified in this way for the 6 tumors is 251495. I did expect this number could be high, but did not expect to be this high.
The number of somatic mutations identified with GATK for tumors with matching normals is 3 or 4 digits for one tumor.
Even with most conservative estimate, the mutation in the tumors without matching normal is 10 times higher.
Is there anyway I can still use the 6 tumors?