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  • gatk indelrealign --known parameter

    hi all
    when using RealignerTargetCreator and IndelRealigner of gatk, both of these two programs have --known parameter.

    if i want to use reads alignment indel information and known indel information such as dbsnp to do the indel realign, how to use --known parameter for RealignerTargetCreator and IndelRealigner ? use this parameter in both of the programs?

    thanks
    Last edited by liuxq; 07-01-2012, 10:19 PM.

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