java.lang.IllegalStateException: Key callStatus found in VariantContext field INFO at 1:762273 but this key isn't defined in the VCFHeader. We require all VCFs to have complete VCF headers by default.

broadinstitute.org | 8 months ago
tip
Do you know that we can give you better hits? Get more relevant results from Samebug’s stack trace search.
  1. 0

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

    broadinstitute.org | 8 months ago
    java.lang.IllegalStateException: Key callStatus found in VariantContext field INFO at 1:762273 but this key isn't defined in the VCFHeader. We require all VCFs to have complete VCF headers by default.

    Root Cause Analysis

    1. java.lang.IllegalStateException

      Key callStatus found in VariantContext field INFO at 1:762273 but this key isn't defined in the VCFHeader. We require all VCFs to have complete VCF headers by default.

      at org.broadinstitute.variant.vcf.VCFEncoder.fieldIsMissingFromHeaderError()
    2. picard
      VCFWriter.add
      1. org.broadinstitute.variant.vcf.VCFEncoder.fieldIsMissingFromHeaderError(VCFEncoder.java:173)
      2. org.broadinstitute.variant.vcf.VCFEncoder.encode(VCFEncoder.java:112)
      3. org.broadinstitute.variant.variantcontext.writer.VCFWriter.add(VCFWriter.java:214)
      3 frames
    3. org.broadinstitute.sting
      CommandLineGATK.main
      1. org.broadinstitute.sting.gatk.io.storage.VariantContextWriterStorage.add(VariantContextWriterStorage.java:183)
      2. org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub.add(VariantContextWriterStub.java:254)
      3. org.broadinstitute.sting.gatk.walkers.validation.GenotypeAndValidate.map(GenotypeAndValidate.java:493)
      4. org.broadinstitute.sting.gatk.walkers.validation.GenotypeAndValidate.map(GenotypeAndValidate.java:216)
      5. org.broadinstitute.sting.gatk.traversals.TraverseLociNano$TraverseLociMap.apply(TraverseLociNano.java:267)
      6. org.broadinstitute.sting.gatk.traversals.TraverseLociNano$TraverseLociMap.apply(TraverseLociNano.java:255)
      7. org.broadinstitute.sting.utils.nanoScheduler.NanoScheduler.executeSingleThreaded(NanoScheduler.java:274)
      8. org.broadinstitute.sting.utils.nanoScheduler.NanoScheduler.execute(NanoScheduler.java:245)
      9. org.broadinstitute.sting.gatk.traversals.TraverseLociNano.traverse(TraverseLociNano.java:144)
      10. org.broadinstitute.sting.gatk.traversals.TraverseLociNano.traverse(TraverseLociNano.java:92)
      11. org.broadinstitute.sting.gatk.traversals.TraverseLociNano.traverse(TraverseLociNano.java:48)
      12. org.broadinstitute.sting.gatk.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:99)
      13. org.broadinstitute.sting.gatk.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:313)
      14. org.broadinstitute.sting.gatk.CommandLineExecutable.execute(CommandLineExecutable.java:121)
      15. org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:248)
      16. org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:155)
      17. org.broadinstitute.sting.gatk.CommandLineGATK.main(CommandLineGATK.java:107)
      17 frames