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.

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via broadinstitute.org by Unknown author, 1 year ago
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.
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(VCFEncoder.java:173)
at org.broadinstitute.variant.vcf.VCFEncoder.encode(VCFEncoder.java:112)
at org.broadinstitute.sting.gatk.io.storage.VariantContextWriterStorage.add(VariantContextWriterStorage.java:183)
at org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub.add(VariantContextWriterStub.java:254)
at org.broadinstitute.sting.gatk.walkers.validation.GenotypeAndValidate.map(GenotypeAndValidate.java:493)
at org.broadinstitute.sting.gatk.walkers.validation.GenotypeAndValidate.map(GenotypeAndValidate.java:216)
at org.broadinstitute.sting.gatk.traversals.TraverseLociNano$TraverseLociMap.apply(TraverseLociNano.java:267)
at org.broadinstitute.sting.gatk.traversals.TraverseLociNano$TraverseLociMap.apply(TraverseLociNano.java:255)
at org.broadinstitute.sting.utils.nanoScheduler.NanoScheduler.executeSingleThreaded(NanoScheduler.java:274)
at org.broadinstitute.sting.utils.nanoScheduler.NanoScheduler.execute(NanoScheduler.java:245)
at org.broadinstitute.sting.gatk.traversals.TraverseLociNano.traverse(TraverseLociNano.java:144)
at org.broadinstitute.sting.gatk.traversals.TraverseLociNano.traverse(TraverseLociNano.java:92)
at org.broadinstitute.sting.gatk.traversals.TraverseLociNano.traverse(TraverseLociNano.java:48)
at org.broadinstitute.sting.gatk.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:99)
at org.broadinstitute.sting.gatk.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:313)
at org.broadinstitute.sting.gatk.CommandLineExecutable.execute(CommandLineExecutable.java:121)
at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:248)
at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:155)
at org.broadinstitute.sting.gatk.CommandLineGATK.main(CommandLineGATK.java:107)

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