Error in Haplotype Caller
Posted in Ask the GATK team | Last updated on 2012-08-07 15:02:38


Comments (19)

Hi,

I am trying to run the latest version (GenomeAnalysisTK-2.0-35-g2d70733) of the HaplotypeCaller on some .bam files that I had prepared according to the Best Practice v.3. Now GATK reports the following error:

ERROR ------------------------------------------------------------------------------------------
ERROR stack trace

java.lang.IllegalArgumentException: Duplicate allele added to VariantContext: T at org.broadinstitute.sting.utils.variantcontext.VariantContext.makeAlleles(VariantContext.java:1328) at org.broadinstitute.sting.utils.variantcontext.VariantContext.(VariantContext.java:304) at org.broadinstitute.sting.utils.variantcontext.VariantContextBuilder.make(VariantContextBuilder.java:518) at org.broadinstitute.sting.gatk.walkers.haplotypecaller.GenotypingEngine.generateVCsFromAlignment(GenotypingEngine.java:604) at org.broadinstitute.sting.gatk.walkers.haplotypecaller.GenotypingEngine.assignGenotypeLikelihoodsAndCallIndependentEvents(GenotypingEngine.java:198) at org.broadinstitute.sting.gatk.walkers.haplotypecaller.HaplotypeCaller.map(HaplotypeCaller.java:414) at org.broadinstitute.sting.gatk.walkers.haplotypecaller.HaplotypeCaller.map(HaplotypeCaller.java:104) at org.broadinstitute.sting.gatk.traversals.TraverseActiveRegions.processActiveRegion(TraverseActiveRegions.java:246) at org.broadinstitute.sting.gatk.traversals.TraverseActiveRegions.callWalkerMapOnActiveRegions(TraverseActiveRegions.java:202) at org.broadinstitute.sting.gatk.traversals.TraverseActiveRegions.processActiveRegions(TraverseActiveRegions.java:177) at org.broadinstitute.sting.gatk.traversals.TraverseActiveRegions.traverse(TraverseActiveRegions.java:134) at org.broadinstitute.sting.gatk.traversals.TraverseActiveRegions.traverse(TraverseActiveRegions.java:27) at org.broadinstitute.sting.gatk.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:62) at org.broadinstitute.sting.gatk.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:269) at org.broadinstitute.sting.gatk.CommandLineExecutable.execute(CommandLineExecutable.java:113) at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:236) at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:146) at org.broadinstitute.sting.gatk.CommandLineGATK.main(CommandLineGATK.java:93)

ERROR ------------------------------------------------------------------------------------------
ERROR A GATK RUNTIME ERROR has occurred (version 2.0-35-g2d70733):
ERROR
ERROR Please visit the wiki to see if this is a known problem
ERROR If not, please post the error, with stack trace, to the GATK forum
ERROR Visit our website and forum for extensive documentation and answers to
ERROR commonly asked questions http://www.broadinstitute.org/gatk
ERROR
ERROR MESSAGE: Duplicate allele added to VariantContext: T
ERROR ------------------------------------------------------------------------------------------

Now I am assuming my old bam files are not compatible with the new HaplotypeCaller. Is that correct?

Thank you for your help, K


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