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Old 05-10-2013, 04:12 AM   #1
dr_sson
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Location: Nederlands

Join Date: Jan 2012
Posts: 1
Default 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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