java.lang.RuntimeException: htsjdk.tribble.TribbleException: The provided VCF file is malformed at approximately line number 3793131: unparsable vcf record with allele 0

GitHub | jrobinso | 2 months ago
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  1. 0

    GitHub comment 362#274199899

    GitHub | 2 months ago | jrobinso
    java.lang.RuntimeException: htsjdk.tribble.TribbleException: The provided VCF file is malformed at approximately line number 3793131: unparsable vcf record with allele 0
  2. 0

    htsjdk.tribble.TribbleException: The provided VCF file is malformed at approximately line number 3793131: unparsable vcf record with allele 0

    GitHub | 2 months ago | mmokrejs
    java.lang.RuntimeException: htsjdk.tribble.TribbleException: The provided VCF file is malformed at approximately line number 3793131: unparsable vcf record with allele 0
  3. 0

    htsjdk.tribble.TribbleException: The provided VCF file is malformed at approximately line number 3793131: unparsable vcf record with allele 0

    GitHub | 2 months ago | mmokrejs
    java.lang.RuntimeException: htsjdk.tribble.TribbleException: The provided VCF file is malformed at approximately line number 3793131: unparsable vcf record with allele 0
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  5. 0

    Ambiguity codes on reference

    GitHub | 2 years ago | inti
    htsjdk.tribble.TribbleException: The provided VCF file is malformed at approximately line number 108: unparsable vcf record with allele S, for input source: /media/TeraData/ipedroso/ANALYSES/DEKKERA/variation/AWRI1499_ref/awri1499_vsawri1499Ref/work/freebayes/AWRI1499_contig1_scaffold1/1-AWRI1499_contig1_scaffold1_0_12137.vcf.gz
  6. 0

    CatVariant not handling allele "*" in gatk-haplotype-joint

    GitHub | 1 year ago | whitejbiii
    htsjdk.tribble.TribbleException: The provided VCF file is malformed at approximately line number 649: unparsable vcf record with allele *, for input source: /media/jawhite/Data/662-exome-trio/work/joint/gatk-haplotype-joint/trio-bwa-j/1/trio-bwa-j-1_0_15543565.vcf.gz

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    Root Cause Analysis

    1. htsjdk.tribble.TribbleException

      The provided VCF file is malformed at approximately line number 3793131: unparsable vcf record with allele 0

      at htsjdk.variant.vcf.AbstractVCFCodec.generateException()
    2. HTS JDK
      AbstractFeatureCodec.decodeLoc
      1. htsjdk.variant.vcf.AbstractVCFCodec.generateException(AbstractVCFCodec.java:784)
      2. htsjdk.variant.vcf.AbstractVCFCodec.checkAllele(AbstractVCFCodec.java:569)
      3. htsjdk.variant.vcf.AbstractVCFCodec.parseSingleAltAllele(AbstractVCFCodec.java:609)
      4. htsjdk.variant.vcf.AbstractVCFCodec.parseAlleles(AbstractVCFCodec.java:539)
      5. htsjdk.variant.vcf.AbstractVCFCodec.parseVCFLine(AbstractVCFCodec.java:336)
      6. htsjdk.variant.vcf.AbstractVCFCodec.decodeLine(AbstractVCFCodec.java:279)
      7. htsjdk.variant.vcf.AbstractVCFCodec.decode(AbstractVCFCodec.java:257)
      8. htsjdk.variant.vcf.AbstractVCFCodec.decode(AbstractVCFCodec.java:60)
      9. htsjdk.tribble.AsciiFeatureCodec.decode(AsciiFeatureCodec.java:79)
      10. htsjdk.tribble.AsciiFeatureCodec.decode(AsciiFeatureCodec.java:41)
      11. htsjdk.tribble.AbstractFeatureCodec.decodeLoc(AbstractFeatureCodec.java:43)
      11 frames
    3. org.broad.igv
      VCFWrapperCodec.decodeLoc
      1. org.broad.igv.feature.tribble.VCFWrapperCodec.decodeLoc(VCFWrapperCodec.java:58)
      2. org.broad.igv.feature.tribble.VCFWrapperCodec.decodeLoc(VCFWrapperCodec.java:43)
      2 frames
    4. HTS JDK
      IndexFactory.createLinearIndex
      1. htsjdk.tribble.index.IndexFactory$FeatureIterator.readNextFeature(IndexFactory.java:502)
      2. htsjdk.tribble.index.IndexFactory$FeatureIterator.next(IndexFactory.java:464)
      3. htsjdk.tribble.index.IndexFactory.createIndex(IndexFactory.java:338)
      4. htsjdk.tribble.index.IndexFactory.createLinearIndex(IndexFactory.java:223)
      4 frames
    5. org.broad.igv
      IgvTools.doIndex
      1. org.broad.igv.tools.IgvTools.createTribbleIndex(IgvTools.java:1062)
      2. org.broad.igv.tools.IgvTools.doIndex(IgvTools.java:981)
      2 frames