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Duplicate Key Error in GATK4 Haplotype Caller


I have been trying to resolve an issue that occurred in some of my samples while running GATK4 Haplotype Caller. After the program has been running for a while, it suddenly stops and this error pops up:

java.lang.IllegalStateException: Duplicate key [[email protected]
at java.util.HashMap.merge(
at java.util.ArrayList$ArrayListSpliterator.forEachRemaining(
at org.broadinstitute.hellbender.engine.AssemblyRegionWalker.processReadShard(
at org.broadinstitute.hellbender.engine.AssemblyRegionWalker.traverse(
at org.broadinstitute.hellbender.engine.GATKTool.doWork(
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(
at org.broadinstitute.hellbender.Main.runCommandLineProgram(
at org.broadinstitute.hellbender.Main.mainEntry(
at org.broadinstitute.hellbender.Main.main(

I have tried removing duplicates using MarkDuplicates but this has not resolved the issue. I was wondering if others were having this issue and what could be causing it.

Thank you in advance for the help


  • shleeshlee CambridgeMember, Broadie ✭✭✭✭✭

    Hi @PhilCharron,

    Perhaps the key refers to elements in a coding dictionary. Could you please post your exact command that produces this error and tell us a little bit about your data. Here are some debugging guidelines that will help us help you:

    1. Try the latest version of tools.
    2. Include tool and Java versions.
    3. Tell us whether you are following GATK Best Practices.
    4. Include relevant details, e.g. platform, DNA- or RNA-Seq, WES (+capture kit) or WGS (PCR-free or PCR+), paired- or single-end, read length, expected average coverage, somatic data, etc.
    5. For tool errors, include the error stacktrace as well as the exact command.
    6. For format issues, include the result of running ValidateSamFile for BAMs or ValidateVariants for VCFs.
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