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Base recalibration & realignment without known sites

gilgigilgi Posts: 19Member
edited October 2012 in Ask the GATK team

Dear GATK team,

Thanks a lot for the new GATK version and GATK forum!

I am trying to use GATK for yeast strains. I do not have files of known sites of SNPs/indels. I understand that the BaseRecalibrator must get such a file. Do you suggest to skip calibration and realignment, or is there another way to go here?

Post edited by Geraldine_VdAuwera on

Best Answer

  • Geraldine_VdAuweraGeraldine_VdAuwera Posts: 6,398Administrator, GATK Developer admin
    edited September 2012 Answer ✓

    Hi Gilgi,

    Glad you like the new digs!

    Skipping Base recalibration and realignment are never a good option. Theere is an article on Base Quality Score Recalibration in the Methods & Workflows section of the Guide that you need to read. Towards the end, in the "Troubleshooting" section, there is a discussion of what to do if you don't have a set of known variants for your organism.

    Good luck!

    Post edited by Geraldine_VdAuwera on

    Geraldine Van der Auwera, PhD

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