Unified Genotyper
Posted in Ask the GATK team | Last updated on


Comments (26)

Hi GATK,

I've seen this error before on the forum associated with the Haplotyper tool, but not with the UnifiedGenotyper. Any thoughts on how I can fix this?

Best,

Alex

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

java.lang.IllegalArgumentException: Duplicate allele added to VariantContext: T at org.broadinstitute.variant.variantcontext.VariantContext.makeAlleles(VariantContext.java:1335) at org.broadinstitute.variant.variantcontext.VariantContext.(VariantContext.java:312) at org.broadinstitute.variant.variantcontext.VariantContextBuilder.make(VariantContextBuilder.java:478) at org.broadinstitute.sting.gatk.walkers.genotyper.ConsensusAlleleCounter.consensusCountsToAlleles(ConsensusAlleleCounter.java:279) at org.broadinstitute.sting.gatk.walkers.genotyper.ConsensusAlleleCounter.computeConsensusAlleles(ConsensusAlleleCounter.java:103) at org.broadinstitute.sting.gatk.walkers.genotyper.IndelGenotypeLikelihoodsCalculationModel.computeConsensusAlleles(IndelGenotypeLikelihoodsCalculationModel.java:93) at org.broadinstitute.sting.gatk.walkers.genotyper.IndelGenotypeLikelihoodsCalculationModel.getInitialAlleleList(IndelGenotypeLikelihoodsCalculationModel.java:245) at org.broadinstitute.sting.gatk.walkers.genotyper.IndelGenotypeLikelihoodsCalculationModel.getLikelihoods(IndelGenotypeLikelihoodsCalculationModel.java:114) at org.broadinstitute.sting.gatk.walkers.genotyper.UnifiedGenotyperEngine.calculateLikelihoods(UnifiedGenotyperEngine.java:320) at org.broadinstitute.sting.gatk.walkers.genotyper.UnifiedGenotyperEngine.calculateLikelihoodsAndGenotypes(UnifiedGenotyperEngine.java:221) at org.broadinstitute.sting.gatk.walkers.genotyper.UnifiedGenotyper.map(UnifiedGenotyper.java:352) at org.broadinstitute.sting.gatk.walkers.genotyper.UnifiedGenotyper.map(UnifiedGenotyper.java:143) at org.broadinstitute.sting.gatk.traversals.TraverseLociNano$TraverseLociMap.apply(TraverseLociNano.java:268) at org.broadinstitute.sting.gatk.traversals.TraverseLociNano$TraverseLociMap.apply(TraverseLociNano.java:256) at org.broadinstitute.sting.utils.nanoScheduler.NanoScheduler.executeSingleThreaded(NanoScheduler.java:274) at org.broadinstitute.sting.utils.nanoScheduler.NanoScheduler.execute(NanoScheduler.java:245) at org.broadinstitute.sting.gatk.traversals.TraverseLociNano.traverse(TraverseLociNano.java:145) at org.broadinstitute.sting.gatk.traversals.TraverseLociNano.traverse(TraverseLociNano.java:92) at org.broadinstitute.sting.gatk.traversals.TraverseLociNano.traverse(TraverseLociNano.java:48) at org.broadinstitute.sting.gatk.executive.ShardTraverser.call(ShardTraverser.java:98) at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:334) at java.util.concurrent.FutureTask.run(FutureTask.java:166) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1110) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:603) at java.lang.Thread.run(Thread.java:722)

ERROR ------------------------------------------------------------------------------------------
ERROR A GATK RUNTIME ERROR has occurred (version 2.4-9-g532efad):
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 ------------------------------------------------------------------------------------------

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