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  • adrian
    Member
    • Oct 2009
    • 90
    #1

    what next after recalibration?

    Hi:
    I am using GATK to call snps. now after running these steps, I am lost. I do not know how to call snps on realigned BAM file.

    CountCovariates -> TableRecalibration -> RealignerTargetCreator.

    what to do after I get realibrated interval file from realigner target creator?

    it is my personal feeling that GATK documentation is cluttered describing last year practices and V2 suggested practice.

    Could someone help please.

    thanks
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