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.

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Solutions on the web26902

  • 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.
  • 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.
  • Key . found in VariantContext field FILTER at 20:61118 but this key isn't defined in the VCFHeader. We require all VCFs to have complete VCF headers by default.
  • Stack trace

    • 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(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.validation.GenotypeAndValidate.map(GenotypeAndValidate.java:496) at org.broadinstitute.gatk.tools.walkers.validation.GenotypeAndValidate.map(GenotypeAndValidate.java:215) 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:121) 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:107)

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