Base Recalibrator Error

AlexanderB

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?

pdexheimer

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.

pdexheimer

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 :)

AlexanderB

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

Geraldine_VdAuwera

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.