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Tumor and normal in a merged bam file
I see some advantages in merging the tumor and normal bam files before gatk realignment. The realn step would benefit from the greater coverge, and one could then run reducereads downstream without potentially losikg coverage in sites with somatic events.
Now to my question: is it possible, or on the horizon, to run mutect on a single bam file, and use differen reads groups (likely the ID part of the @RG tag) to variant?