htsjdk.tribble.TribbleException$MalformedFeatureFile: Unable to parse header with error: Your input file has a malformed header: We never saw the required CHROM header line (starting with one #) for the input VCF file, for input source: /project/ibilab/projects/Devraj_Basu_HNSCC_Devraj_2016_3/large_data/bcbio-result5/work/mutect2/chr17/720-chr17_78458800_81195210.vcf.gz

GitHub | hyong2000 | 9 months ago
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  1. 0

    GitHub comment 1199#233337867

    GitHub | 9 months ago | hyong2000
    htsjdk.tribble.TribbleException$MalformedFeatureFile: Unable to parse header with error: Your input file has a malformed header: We never saw the required CHROM header line (starting with one #) for the input VCF file, for input source: /project/ibilab/projects/Devraj_Basu_HNSCC_Devraj_2016_3/large_data/bcbio-result5/work/mutect2/chr17/720-chr17_78458800_81195210.vcf.gz
  2. 0

    tumor-only calling issue

    GitHub | 1 year ago | parlar
    htsjdk.tribble.TribbleException$MalformedFeatureFile: Unable to parse header with error: Your input file has a malformed header: We never saw the required CHROM header line (starting with one #) for the input VCF file, for input source: /home/genetik/irina/myeloid_fastq_run/calling/work/mutect/chr7/16-0206-chr7_50367205_101459534.vcf.gz

    Root Cause Analysis

    1. htsjdk.tribble.TribbleException$InvalidHeader

      Your input file has a malformed header: We never saw the required CHROM header line (starting with one #) for the input VCF file

      at htsjdk.variant.vcf.VCFCodec.readActualHeader()
    2. HTS JDK
      AbstractFeatureReader.getFeatureReader
      1. htsjdk.variant.vcf.VCFCodec.readActualHeader(VCFCodec.java:119)
      2. htsjdk.tribble.AsciiFeatureCodec.readHeader(AsciiFeatureCodec.java:88)
      3. htsjdk.tribble.AsciiFeatureCodec.readHeader(AsciiFeatureCodec.java:41)
      4. htsjdk.tribble.TabixFeatureReader.readHeader(TabixFeatureReader.java:88)
      5. htsjdk.tribble.TabixFeatureReader.<init>(TabixFeatureReader.java:74)
      6. htsjdk.tribble.AbstractFeatureReader.getFeatureReader(AbstractFeatureReader.java:85)
      7. htsjdk.tribble.AbstractFeatureReader.getFeatureReader(AbstractFeatureReader.java:66)
      7 frames
    3. org.broadinstitute.gatk
      CatVariants.main
      1. org.broadinstitute.gatk.tools.CatVariants.getFeatureReader(CatVariants.java:188)
      2. org.broadinstitute.gatk.tools.CatVariants.execute(CatVariants.java:280)
      3. org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:248)
      4. org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:155)
      5. org.broadinstitute.gatk.tools.CatVariants.main(CatVariants.java:312)
      5 frames