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Where do I get missing walkers?

giorgiopeagiorgiopea Member
edited October 2012 in Ask the GATK team

I've downloaded both the full and the Lite version of GATK 2.0. In both cases the available java files in the folder "resources" are the following:

CountLoci; DepthOfCoverage; Pileup; ValidatingPileup; CountReads; PrintReads

Do these correspond to the actually available walkers in my installation?
If so, is there a way to get the other GATK walkers? I have non-commercial purposes and was planning to test some pipelines, so actually any version would do.

Thank you,


Best Answer

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MA admin
    Accepted Answer

    All the walkers are contained in the main GenomeAnalysisTK.jar file. You don't ned to pay attention to those resources files. The only walkers that are not included in the lite version are ReduceReads and HaplotypeCaller; those are contained in the full version.


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