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BaseRecalibration or IndelRealignment first?

mikedmiked Member
edited January 2013 in Ask the GATK team


I asked this question in a comment under BestPractices but never got a response. Hopefully I will here. Here goes:

I have been running GATK v1.6.2 on several samples. It seems the way I had initially had run GATK for indel-realignment and quality re-calibration steps are reversed. For example, in order of processing, I ran:

  • MarkDuplicates
  • Count Covariates
  • Table Recalibration
  • Realigner Target Creator
  • Indel Realigner

What are the consequences and effect to SNP and INDEL calling if the GATK steps are ran as above?. I'm aware that this is not according to the best-practices document (thank you for the thorough GATK documentation), but I wanted to know if it is essential for me to re-analyze the samples. The variant caller I'm using looks at BaseQuality scores when making calls.

Any help on this would be appreciated.


Post edited by Geraldine_VdAuwera on


  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    Hi Mike,

    Your question slipped through our response net, sorry about that. The official answer is: we've answered this question before, please search the forum for this info. The nicer answer is that the order of realignment and recalibration shouldn't make much difference, so you don't really need to worry about it.

    If you did decide to run your samples through again, consider upgrading to the latest version (currently 2.2) which is faster and better...

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