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can you recommend a great tutorial on "processing-for-variant-discovery-gatk4" with different read groups/lanes on terra?


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    Beri Shifaw

    The requirements in the workflow WDL header states 

    ## Requirements/expectations :
    ## - Pair-end sequencing data in unmapped BAM (uBAM) format
    ## - One or more read groups, one per uBAM file, all belonging to a single sample (SM)
    ## - Input uBAM files must additionally comply with the following requirements:
    ## - - filenames all have the same suffix (we use ".unmapped.bam")
    ## - - files must pass validation by ValidateSamFile
    ## - - reads are provided in query-sorted order
    ## - - all reads must have an RG tag


    You should be able to provide the workflow any ubam from different readgroups as long as it's the same sample. So in your case you would run the workflow twice, once providing all ubams associated with the tumor sample and a second time for all the ubams associated with the normal sample

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