Bug Bulletin: The GenomeLocPArser error in SplitNCigarReads has been fixed; if you encounter it, use the latest nightly build.

Base Recalibrator Error

AlexanderBAlexanderB Posts: 17Member
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 Posts: 345 ✭✭✭
    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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