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

GitHub | fleharty | 3 months ago
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  1. 0

    GenotypeConcordance is not aware of spanning deletions

    GitHub | 3 months ago | fleharty
    java.lang.IllegalArgumentException: Unexpected base in allele bases '*ATAT'
  2. 0

    GenotypeConcordance dies if both samples are no call

    GitHub | 2 months ago | apregier
    java.lang.IllegalArgumentException: BUG: Cannot add a no call allele to a variant context [TA*, .] this=[VC Unknown @ chr1:53707-53708 Q584.04 of type=INDEL alleles=[TA*, .] attr={CONC_ST=[EMPTY]} GT=[[call ./. DP 1 AD 1,0],[truth ./. DP 1 AD 1,0]]
  3. 0

    Illegal base [ ] seen in the allele; seemingly random error

    GitHub | 2 years ago | stsmall
    java.lang.IllegalArgumentException: Illegal base [ ] seen in the allele
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  5. 0

    Null alleles error.

    GitHub | 1 year ago | ankushreddy
    java.lang.IllegalArgumentException: Null alleles are not supported
  6. 0

    Ambiguity codes on reference

    GitHub | 3 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

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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