Bug Bulletin: we have identified a bug that affects indexing when producing gzipped VCFs. This will be fixed in the upcoming 3.2 release; in the meantime you need to reindex gzipped VCFs using Tabix.

BaseRecalibration or IndelRealignment first?

mikedmiked Posts: 2Member
edited January 2013 in Ask the team

Hello,

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.

Mike

Post edited by Geraldine_VdAuwera on

Answers

  • Geraldine_VdAuweraGeraldine_VdAuwera Posts: 5,285Administrator, GSA Member 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...

    Geraldine Van der Auwera, PhD

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