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How does GATK4 Mutect2 know which -I is tumor?


I'm reading the Mutect2 documentation here:


I see that you give two -I arguments. How does Mutect2 know which is the tumor? Is it whichever comes first, or is it related to the placement of the -tumor argument?


Best Answer


  • Nevermind, I think I understand. It's actually using the SM tag on the reads, right? So I could even put the tumor and normal in one BAM file, and just have one -I argument, and it will sort them out by looking for SM tags matching the -tumor and -normal arguments I gave.

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