java.lang.IllegalStateException: Key callStatus found in VariantContext field INFO at chrM:3506 but this key isn't defined in the VCFHeader. We require all VCFs to have complete VCF headers by default.

broadinstitute.org | 3 months ago
  1. 0

    GenotypeAndValidate error: Key callStatus found in VariantContext field INFO — GATK-Forum

    broadinstitute.org | 3 months ago
    java.lang.IllegalStateException: Key callStatus found in VariantContext field INFO at chrM:3506 but this key isn't defined in the VCFHeader. We require all VCFs to have complete VCF headers by default.
  2. 0

    (howto) Run the genotype refinement workflow - GATK-Forum

    broadinstitute.org | 1 year ago
    java.lang.IllegalStateException: Key OLD_VARIANT found in VariantContext field INFO at X:7151130 but this key isn't defined in the VCFHeader. We require all VCFs to have complete VCF headers by default.
  3. 0

    GATK | GATK | Tagged #genotypegvcfs

    broadinstitute.org | 8 months ago
    java.lang.IllegalStateException: Key DP found in VariantContext field INFO at 1:4839315 but this key isn't defined in the VCFHeader. We require all VCFs to have complete VCF headers by default.
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  5. 0

    Exception in thread "main" java.lang.IllegalStateException: Key found in VariantContext field INFO at 1:949696 but this key isn't defined in the VCFHeader. We require all VCFs to have complete VCF headers by default.

    GitHub | 2 years ago | leipzig
    java.lang.IllegalStateException: Key found in VariantContext field INFO at 1:949696 but this key isn't defined in the VCFHeader. We require all VCFs to have complete VCF headers by default.
  6. 0

    key REJECT found in VariantContext field FILTER

    GitHub | 10 months ago | apastore
    java.lang.IllegalStateException: Key REJECT found in VariantContext field FILTER at chrY:21877584 but this key isn't defined in the VCFHeader. We require all VCFs to have complete VCF headers by default.

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    Root Cause Analysis

    1. java.lang.IllegalStateException

      Key callStatus found in VariantContext field INFO at chrM:3506 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()
    2. HTS JDK
      VCFWriter.add
      1. htsjdk.variant.vcf.VCFEncoder.fieldIsMissingFromHeaderError(VCFEncoder.java:176)
      2. htsjdk.variant.vcf.VCFEncoder.encode(VCFEncoder.java:115)
      3. htsjdk.variant.variantcontext.writer.VCFWriter.add(VCFWriter.java:221)
      3 frames
    3. org.broadinstitute.gatk
      CommandLineGATK.main
      1. org.broadinstitute.gatk.engine.io.storage.VariantContextWriterStorage.add(VariantContextWriterStorage.java:182)
      2. org.broadinstitute.gatk.engine.io.stubs.VariantContextWriterStub.add(VariantContextWriterStub.java:269)
      3. org.broadinstitute.gatk.tools.walkers.validation.GenotypeAndValidate.map(GenotypeAndValidate.java:496)
      4. org.broadinstitute.gatk.tools.walkers.validation.GenotypeAndValidate.map(GenotypeAndValidate.java:215)
      5. org.broadinstitute.gatk.engine.traversals.TraverseLociNano$TraverseLociMap.apply(TraverseLociNano.java:267)
      6. org.broadinstitute.gatk.engine.traversals.TraverseLociNano$TraverseLociMap.apply(TraverseLociNano.java:255)
      7. org.broadinstitute.gatk.utils.nanoScheduler.NanoScheduler.executeSingleThreaded(NanoScheduler.java:274)
      8. org.broadinstitute.gatk.utils.nanoScheduler.NanoScheduler.execute(NanoScheduler.java:245)
      9. org.broadinstitute.gatk.engine.traversals.TraverseLociNano.traverse(TraverseLociNano.java:144)
      10. org.broadinstitute.gatk.engine.traversals.TraverseLociNano.traverse(TraverseLociNano.java:92)
      11. org.broadinstitute.gatk.engine.traversals.TraverseLociNano.traverse(TraverseLociNano.java:48)
      12. org.broadinstitute.gatk.engine.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:99)
      13. org.broadinstitute.gatk.engine.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:319)
      14. org.broadinstitute.gatk.engine.CommandLineExecutable.execute(CommandLineExecutable.java:121)
      15. org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:248)
      16. org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:155)
      17. org.broadinstitute.gatk.engine.CommandLineGATK.main(CommandLineGATK.java:107)
      17 frames