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GATK runtime error stack trace when running SelectVariants ("This might be a bug")

noanoa Boston areaMember

I am trying to run Select variants with a list of targeted regions and receiving the following message.
I'm using version 2014.4-3.3.0-0-ga3711aa
I prefer not to upgrade to a newer version right now unless necessary.
Any help will be appreciated, Thanks.

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

java.lang.IllegalStateException: Key PLNCIIonWG found in VariantContext field INFO at 4:55141055 but this key isn't defined in the VCFHeader. We require all VCFs to have complete VCF headers by default.
at htsjdk.variant.vcf.VCFEncoder.fieldIsMissingFromHeaderError(VCFEncoder.java:176)
at htsjdk.variant.vcf.VCFEncoder.encode(VCFEncoder.java:115)
at htsjdk.variant.variantcontext.writer.VCFWriter.add(VCFWriter.java:221)
at org.broadinstitute.gatk.engine.io.storage.VariantContextWriterStorage.add(VariantContextWriterStorage.java:182)
at org.broadinstitute.gatk.engine.io.stubs.VariantContextWriterStub.add(VariantContextWriterStub.java:269)
at org.broadinstitute.gatk.tools.walkers.variantutils.SelectVariants.map(SelectVariants.java:532)
at org.broadinstitute.gatk.tools.walkers.variantutils.SelectVariants.map(SelectVariants.java:182)
at org.broadinstitute.gatk.engine.traversals.TraverseLociNano$TraverseLociMap.apply(TraverseLociNano.java:267)
at org.broadinstitute.gatk.engine.traversals.TraverseLociNano$TraverseLociMap.apply(TraverseLociNano.java:255)
at org.broadinstitute.gatk.utils.nanoScheduler.NanoScheduler.executeSingleThreaded(NanoScheduler.java:274)
at org.broadinstitute.gatk.utils.nanoScheduler.NanoScheduler.execute(NanoScheduler.java:245)
at org.broadinstitute.gatk.engine.traversals.TraverseLociNano.traverse(TraverseLociNano.java:144)
at org.broadinstitute.gatk.engine.traversals.TraverseLociNano.traverse(TraverseLociNano.java:92)
at org.broadinstitute.gatk.engine.traversals.TraverseLociNano.traverse(TraverseLociNano.java:48)
at org.broadinstitute.gatk.engine.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:99)
at org.broadinstitute.gatk.engine.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:319)
at org.broadinstitute.gatk.engine.CommandLineExecutable.execute(CommandLineExecutable.java:126)
at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:248)
at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:155)
at org.broadinstitute.gatk.engine.CommandLineGATK.main(CommandLineGATK.java:108)

ERROR ------------------------------------------------------------------------------------------
ERROR A GATK RUNTIME ERROR has occurred (version 2014.4-3.3.0-0-ga3711aa):
ERROR This might be a bug. Please check the documentation guide to see if this is a known problem.
ERROR Visit our website for extensive documentation and answers to
ERROR commonly asked questions http://gatkdocs.appistry.com/
ERROR MESSAGE: Key PLNCIIonWG found in VariantContext field INFO at 4:55141055 but this key isn't defined in the VCFHeader. We require all VCFs to have complete VCF headers by default.


  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    Was your VCF processed with non GATK tools? Some third party tools fail to add annotation definitions in the header. This is technically legal by the VCF specification but GATK considers it a malformation.

    The simplest solution is to add header lines manually for the additional annotations.

  • noanoa Boston areaMember

    I actually used a vcf of na12878 downloaded from this link:

    as far as I can see it looks ok and I didn't notice anything unusual in chr4 from which the error came. The header looks like that:



    Do you recognize any problem with that?
    Thanks again,

  • SheilaSheila Broad InstituteMember, Broadie ✭✭✭✭✭

    Hi Noa,

    You just have to add a description of the annotation in the header. For example, if the annotation that was missing was AD, you would add

    FORMAT=<ID=AD,Number=.,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed"> to the header.

    I hope this helps.


  • noanoa Boston areaMember

    Hi Shila,
    It did help - I added the following line to the header and it's running:
    '##INFO=<ID=PLNCIIonWG,Number=.,Type=String,Description="Genotype likelihoods for Ion">\n'
    in case other people run into it too.
    Thanks a lot,

  • mglclinicalmglclinical USAMember

    I had the same issue, and I fixed my NIST vcf file

    thanks for the answers here @Sheila and @noa

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