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Picard 2.10.2 is now available at https://github.com/broadinstitute/picard/releases.
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Base Recalibrator Error

AlexanderBAlexanderB Member
edited January 2013 in Ask the GATK team

Sorry to post such a simple question but I seem to be at my wits end. Base Recalibrator keeps giving me this error:

ERROR ------------------------------------------------------------------------------------------
ERROR A USER ERROR has occurred (version 2.0-36-gf5c1c1a):
ERROR
ERROR MESSAGE: The platform (HiSeq2000) associated with read group org.broadinstitute.sting.utils.sam.GATKSAMReadGroupRecord@32 is not a recognized platform. Implemented options are e.g. illumina, 454, and solid
ERROR ------------------------------------------------------------------------------------------

Why isn't HiSeq2000 recognized as Illumina?

Post edited by Geraldine_VdAuwera on

Best Answer

  • pdexheimerpdexheimer Member, Dev
    Accepted Answer

    This would be outside the scope of GATK. The simplest (though not quickest) way to change it would be to convert the file to SAM, manually edit the @RG tag and save it, then convert back to BAM. I would use samtools, though I think you could do the same thing with Picard.

    A more efficient method would be to use the "reheader" functionality that samtools and picard both offer, though that's a little bit more complicated.

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