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  • dr_sson
    Junior Member
    • Jan 2012
    • 1

    #1

    Which GATK step should be multisample?

    Hi everybody,
    I am new in NGS analysis and hope not to ask something already solved (or discussed), in that case please only refer me to the right discussion.
    I am writing an analysis pipeline, based on gatk, to analyse exome data.
    My question is: which step of the gatk is better to do on multiple samples?
    I figured out the following pipeline up to the UnifiedGenotyper:
    dedupplig (single sample) ->
    RealignTargetCreator (multiple) ->
    IndelRealigner (single) ->
    BaseRecalibrator (multiple) ->
    UnifiedGenotyper (multiple)

    Is this correct?

    Thank you

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