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Error on Running HaplotypeCaller

Hi Team
I am trying to output all genotype calls on chr6 based on a given set of snps.

I keep getting this message after the run finishes 0.1%.
Is this error already solved in new version? or is this something that might have resulted from my files?

Thanks
-Biju

version info>>
GATK Version 3.5-0-g36282e4

command used>>
GenomeAnalysisTK.jar -R ucsc.hg19.fasta -T HaplotypeCaller -I [in.bam] -gt_mode GENOTYPE_GIVEN_ALLELES --alleles dbsnp.chr6.vcf -L dbsnp.chr6.vcf -ip 150 -o output.vcf -stand_call_conf 0 -stand_emit_conf 0 -nt 1 -nct 2

error message>>
java.lang.IndexOutOfBoundsException: Index: 3, Size: 3
at java.util.ArrayList.rangeCheck(ArrayList.java:653)
at java.util.ArrayList.get(ArrayList.java:429)
at htsjdk.variant.variantcontext.VariantContext.getAlternateAllele(VariantContext.java:886)
at org.broadinstitute.gatk.tools.walkers.haplotypecaller.HaplotypeCallerGenotypingEngine.assignGenotypeLikelihoods(HaplotypeCallerGenotypingEngine.java:252)
at org.broadinstitute.gatk.tools.walkers.haplotypecaller.HaplotypeCaller.map(HaplotypeCaller.java:924)
at org.broadinstitute.gatk.tools.walkers.haplotypecaller.HaplotypeCaller.map(HaplotypeCaller.java:228)
at org.broadinstitute.gatk.engine.traversals.TraverseActiveRegions$TraverseActiveRegionMap.apply(TraverseActiveRegions.java:709)
at org.broadinstitute.gatk.engine.traversals.TraverseActiveRegions$TraverseActiveRegionMap.apply(TraverseActiveRegions.java:705)
at org.broadinstitute.gatk.utils.nanoScheduler.NanoScheduler$ReadMapReduceJob.run(NanoScheduler.java:471)
at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)
at java.util.concurrent.FutureTask.run(FutureTask.java:266)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
at java.lang.Thread.run(Thread.java:745)

ERROR ------------------------------------------------------------------------------------------
ERROR A GATK RUNTIME ERROR has occurred (version 3.5-0-g36282e4):
ERROR
ERROR This might be a bug. Please check the documentation guide to see if this is a known problem.
ERROR If not, please post the error message, 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: Index: 3, Size: 3

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