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Mutect2 paired tumor/normal must be same design ?
Hi GATK team !
While trying to test MuTecT2 intensively on some of my samples, I was wondering about the requirements that you would make on the pair tumor/normal.
For example I have here some normal samples that have are capture-sequenced on a panel of 30 genes.
However my tumor samples come from amplicon sequencing on only 2 genes (included in the 30 above, obviously).
For this amplicon design, I trim the primers and do not mark duplicates.
However, could that (the difference in design and the difference in target size) mislead the results in any way ? Are there some parameters that I should adjust ? (minPruning ? kmers ? others ?).
Thank you for your answer.