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Using GATK as a library

deechdeech Member
edited July 2012 in Ask the GATK team

Hi all,
We are using GATK as part of our internal pipelines written in Java. Currently we are making command-line calls to the GenomeAnalysisTk jar, but this generated intermediate files and it would be better if we could just directly call the relevant functions in the target and hold the results in memory. Reading the source it is not immediately obvious so I was hoping for some guidance. As an example of a how we use it as part of our pipeline:
java -jar GenomeAnalysisTK.jar -T RealignerTargetCreator -R -I -o
java -jar GenomeAnalysisTK.jar -T IndelRealigner -R -targetIntervals -I --o <realigned.ban>



  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    Hi there,

    I'm afraid that's not currently possible, so we can't help you with this. You can always try posting in the "Ask the community" category and see if someone out there can think of a way to implement that functionality. If so we'd love to hear about it!

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