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Mutect2 not detecting variant visible in tumor and matched cell line bam
I am unable to detect a particular variant when running Mutect2 on a tumor and tumor-derived cell line exome data. I ran each with the corresponding matched normal. The image below displays, from top to bottom: 1) input bam of cell line 2) bamout of cell line 3) input bam of tumor 4) bamout of tumor.
I have had some success in cases where mutect2 didn't detect a visible variant by running again with a focal interval file. No such luck here. Do you have guidance on troubleshooting?