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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.variant.variantcontext.writer.VCFWriter.add(VCFWriter.java:214) 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)