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Labels

54 labels

  • alpha_sat

    alpha_sat
    At least part of region is annotated as alpha satellite sequence

  • at

    at
    Region of high AT content

  • base_error

    base_error
    short error in base, low quality consensus

  • clipped

    clipped
    Region contains reads with high level of clipping

  • correction_applied

    correction_applied
    Correction applied in next assembly version

  • correction_pending

    correction_pending
    A correction for this issue will be applied in the next release

  • coverage_pri

    coverage_pri
    Issues discovered by primary alignments of reads to assembly

  • deferred

    deferred
    Correction deferred until next assembly release

  • duplicate

    duplicate
    These issues are duplicates of other issues

  • element_evidence

    element_evidence
    Based on a variant called from Element alignments

  • error_kmer

    error_kmer
    Assembly contains kmers not present in the (hybrid) set of reads

  • false_positive

    false_positive
    Not likely to be an assembly error

  • flagger_intersect

    flagger_intersect
    Intersects flagger calls from both HiFi and ONT reads

  • ga_tc

    ga_tc
    Region of high GA/TC content

  • gc

    gc
    Region of high GC content

  • geno_01

    geno_01
    Child has 0/1 genotype w.r.t. this haplotype

  • geno_02

    geno_02

  • geno_12

    geno_12
    Child has 1/2 genotype w.r.t. this haplotype

  • haplotype_switch

    haplotype_switch
    haplotype switch

  • help_wanted

    help_wanted
    Extra attention is needed

  • hifi_evidence

    hifi_evidence
    This issue has evidence in the HiFi reads

  • high_cov_hifi

    high_cov_hifi
    Region with higher than expected HiFi coverage (possible collapse)

  • high_cov_ont

    high_cov_ont
    Region with higher than expected ONT coverage (possible collapse)

  • homopolymer

    homopolymer

  • hsat2

    hsat2
    At least part of region is annotated HSat2

  • hsat3

    hsat3
    At least part of region is annotated HSat3

  • invalid

    invalid
    This doesn't seem right

  • large_error

    large_error
    This issue describes a poor quality or misassembled region in the assembly

  • longread_homnonref

    longread_homnonref
    Issue discovered from homozygous non-reference DeepVariant calls on long read data

  • longread_missinghet

    longread_missinghet
    False homozygosity in assembly discovered by DeepVariant hom non ref call on aligns to both haps