java.lang.IllegalStateException

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.

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Stack trace

  • java.lang.IllegalStateException: 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. at htsjdk.variant.vcf.VCFEncoder.fieldIsMissingFromHeaderError(VCFEncoder.java:173) at htsjdk.variant.vcf.VCFEncoder.getFilterString(VCFEncoder.java:154) at htsjdk.variant.vcf.VCFEncoder.encode(VCFEncoder.java:106) at htsjdk.variant.variantcontext.writer.VCFWriter.add(VCFWriter.java:222)

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