Meaning of error: expected haplotypes.size() >= eventsAtThisLoc.size() + 1

mrooneymrooney Cambridge, MAMember

Hi, I am running HaplotypeCaller (GATK 4.0.0.0) in genoype-given-alleles mode using a VCF of common coding germline variants. Please see the error below. Can anyone help to point me in the right direction? Thanks!

java.lang.IllegalArgumentException: expected haplotypes.size() >= eventsAtThisLoc.size() + 1
at org.broadinstitute.hellbender.utils.Utils.validateArg(Utils.java:681)
at org.broadinstitute.hellbender.tools.walkers.haplotypecaller.AssemblyBasedCallerGenotypingEngine.createAlleleMapper(AssemblyBasedCallerGenotypingEngine.java:159)
at org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCallerGenotypingEngine.assignGenotypeLikelihoods(HaplotypeCallerGenotypingEngine.java:123)
at org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCallerEngine.callRegion(HaplotypeCallerEngine.java:566)
at org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCaller.apply(HaplotypeCaller.java:218)
at org.broadinstitute.hellbender.engine.AssemblyRegionWalker.processReadShard(AssemblyRegionWalker.java:295)
at org.broadinstitute.hellbender.engine.AssemblyRegionWalker.traverse(AssemblyRegionWalker.java:271)
at org.broadinstitute.hellbender.engine.GATKTool.doWork(GATKTool.java:893)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:136)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:179)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:198)
at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:152)
at org.broadinstitute.hellbender.Main.mainEntry(Main.java:195)
at org.broadinstitute.hellbender.Main.main(Main.java:275)

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