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.

GitHub | pabarcgar | 4 months ago
  1. 0

    Exception in VCFEncoder when trying to write a missing value in the VCF "Filter" column

    GitHub | 4 months ago | pabarcgar
    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.
  2. 0

    GitHub comment 1276#261126595

    GitHub | 3 weeks ago | heuermh
    java.lang.IllegalStateException: Key IndelQD found in VariantContext field FILTER at 1:14397 but this key isn't defined in the VCFHeader. We require all VCFs to have complete VCF headers by default.
  3. 0

    Exception in thread "main" java.lang.IllegalStateException: 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.

    GitHub | 2 years ago | leipzig
    java.lang.IllegalStateException: 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.
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  5. 0

    (howto) Run the genotype refinement workflow - GATK-Forum

    broadinstitute.org | 1 year ago
    java.lang.IllegalStateException: Key OLD_VARIANT found in VariantContext field INFO at X:7151130 but this key isn't defined in the VCFHeader. We require all VCFs to have complete VCF headers by default.
  6. 0

    key REJECT found in VariantContext field FILTER

    GitHub | 11 months ago | apastore
    java.lang.IllegalStateException: Key REJECT found in VariantContext field FILTER at chrY:21877584 but this key isn't defined in the VCFHeader. We require all VCFs to have complete VCF headers by default.

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    Root Cause Analysis

    1. 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()
    2. HTS JDK
      VCFWriter.add
      1. htsjdk.variant.vcf.VCFEncoder.fieldIsMissingFromHeaderError(VCFEncoder.java:173)
      2. htsjdk.variant.vcf.VCFEncoder.getFilterString(VCFEncoder.java:154)
      3. htsjdk.variant.vcf.VCFEncoder.encode(VCFEncoder.java:106)
      4. htsjdk.variant.variantcontext.writer.VCFWriter.add(VCFWriter.java:222)
      4 frames