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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?



  • kcibulkcibul Cambridge, MAMember, Broadie, Dev ✭✭✭


    yes -- there is great advantage in combining tumor and normal data for the local realignment step, and it's something we recommend. However, after that step you must spit the BAMs back out again. It's currently not possible to do call on BAM containing both Tumor and Normal together, although I agree it would be a good extension to make in a future version.

  • dklevebringdklevebring Member

    Ok, thanks. I think a syntax like T="1005T1,1005T2" N="1005N1,1005N2" would be great in order to specify several read groups (for example from several libraries per sample) for tumor and normal. Just my two cents :)

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