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Base Recalibrator Error

AlexanderBAlexanderB Member Posts: 17
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 Posts: 543 ✭✭✭✭
    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.

Answers

  • pdexheimerpdexheimer Member, Dev Posts: 543 ✭✭✭✭

    Because GATK doesn't have NLP. it doesn't have a dictionary or anything of manufacturer -> model, and in fact doesn't even have a concept of manufacturer or model. They're just strings. Set it to Illumina and move on :)

  • AlexanderBAlexanderB Member Posts: 17

    Excellent! Thank you very much for the speedy reply. But what is the syntax option to do so?

  • pdexheimerpdexheimer Member, Dev Posts: 543 ✭✭✭✭
    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.

  • Geraldine_VdAuweraGeraldine_VdAuwera Administrator, Dev Posts: 10,993 admin

    To clarify further, it's not something you specify in your command-line; it should be written in the PL field in the BAM header (as indicated in the article on input files). See @pdexheimer's suggestions for how to do this.

    Geraldine Van der Auwera, PhD

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