java.lang.IllegalArgumentException: Unexpected base in allele bases '*ATAT'

GitHub | fleharty | 2 months ago
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    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
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    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

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    Root Cause Analysis

    1. java.lang.IllegalArgumentException

      Unexpected base in allele bases '*ATAT'

      at htsjdk.variant.variantcontext.Allele.<init>()
    2. HTS JDK
      Allele.create
      1. htsjdk.variant.variantcontext.Allele.<init>(Allele.java:162)
      2. htsjdk.variant.variantcontext.Allele.create(Allele.java:234)
      3. htsjdk.variant.variantcontext.Allele.create(Allele.java:355)
      3 frames
    3. picard.vcf
      GenotypeConcordance.lambda$doWork$39
      1. picard.vcf.GenotypeConcordance$Alleles.asList(GenotypeConcordance.java:641)
      2. picard.vcf.GenotypeConcordance.writeVcfTuple(GenotypeConcordance.java:431)
      3. picard.vcf.GenotypeConcordance.lambda$doWork$39(GenotypeConcordance.java:333)
      3 frames