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Interpreting TRGT-denovo output

Missing values are denoted by: ., indicating that a given locus has a missing genotype in at least one sample, or a locus is skipped because of quick mode.

Trio fields:

  • trid ID of the tandem repeat, encoded as in the BED file
  • genotype Genotype ID of the child for a specific allele, corresponds to the TRGT genotype ID
  • denovo_coverage Number of child reads supporting a de novo allele compared to parental data
  • allele_coverage Number of child reads mapped to this specific allele
  • allele_ratio Ratio of de novo coverage to allele coverage
  • child_coverage Total number of child reads at this site
  • child_ratio Ratio of de novo coverage to total coverage at this site
  • mean_diff_father Score difference between de novo and paternal reads; lower values indicate greater similarity
  • mean_diff_mother Score difference between de novo and maternal reads; lower values indicate greater similarity
  • father_dropout_prob Dropout rate for reads coming from the mother
  • mother_dropout_prob Dropout rate for reads coming from the father.
  • allele_origin Inferred origin of the allele based on alignment; possible values: {F:{1,2,?}, M:{1,2,?}, ?}. F and M denote father and mother respectively. The associated {1, 2, ?} values denote the first or second allele from either parent or ? when this cannot be derived unambiguously. Lastly a ? denotes an allele for which parental origin cannot be determined unambiguously
  • denovo_status Indicates if the allele is de novo, only if allele_origin is defined; possible values: {., X, Y:{+, -, =, ?}}. This is . if there is a missing value, X if no de novo read is found and Y otherwise, if parental origin can be determined without ambiguity the allele sequences can be compared directly such that the de novo type can be established as + (expansion), - (contraction), = (substitution), ? if allele_origin is not defined
  • per_allele_reads_father Number of reads partitioned per allele in the father (allele1, allele2)
  • per_allele_reads_mother Number of reads partitioned per allele in the mother (allele1, allele2)
  • per_allele_reads_child Number of reads partitioned per allele in the child (allele1, allele2)
  • father_dropout Coverage cut-off dropout detection using HP tags from phasing tools in father; possible values: Full dropout (FD), Haplotype dropout (HD), Not (N)
  • mother_dropout Coverage cut-off dropout detection using HP tags from phasing tools in mother; possible values: Full dropout (FD), Haplotype dropout (HD), Not (N)
  • child_dropout Coverage cut-off dropout detection using HP tags from phasing tools in child; possible values: Full dropout (FD), Haplotype dropout (HD), Not (N)
  • index Index of this allele in the TRGT VCF
  • father_MC TRGT VCF motif counts for this locus in the father
  • mother_MC TRGT VCF motif counts for this locus in the mother
  • child_MC TRGT VCF motif counts for this locus in the child
  • father_AL TRGT VCF allele lengths for this locus in the father
  • mother_AL TRGT VCF allele lengths for this locus in the mother
  • child_AL TRGT VCF allele lengths for this locus in the child
  • father_overlap_coverage Reciprocal of denovo_coverage, the number of reads in per allele in the father that overlap compared to the child data
  • mother_overlap_coverage Reciprocal of denovo_coverage, the number of reads in per allele in the mother that overlap compared to the child data

Duo fields:

  • trid ID of the tandem repeat, encoded as in the BED file
  • genotype Genotype ID of sample A for a specific allele, corresponds to the TRGT genotype ID
  • denovo_coverage Number of sample A reads supporting a de novo allele compared to sample B
  • allele_coverage Number of sample A reads mapped to this specific allele
  • allele_ratio Ratio of de novo coverage to allele coverage
  • a_coverage Total number of sample A reads at this site
  • a_ratio Ratio of de novo coverage to total coverage at this site
  • mean_diff_b Score difference between de novo and sample B reads; lower values indicate greater similarity
  • denovo_status Attempts to say if the allele is de novo; possible values: {., X, Y:{?}}. This is . if there is a missing value, X if not a single de novo read is found and Y:? otherwise.
  • per_allele_reads_a Number of reads partitioned per allele in sample A (allele1, allele2)
  • per_allele_reads_b Number of reads partitioned per allele in sample B (allele1, allele2)
  • a_dropout Coverage cut-off dropout detection using HP tags from phasing tools in sample A; possible values: Full dropout (FD), Haplotype dropout (HD), Not (N)
  • b_dropout Coverage cut-off dropout detection using HP tags from phasing tools in sample B; possible values: Full dropout (FD), Haplotype dropout (HD), Not (N)
  • index Index of this allele in the TRGT VCF
  • a_MC TRGT VCF motif counts for this locus in sample A
  • b_MC TRGT VCF motif counts for this locus in sample B
  • a_AL TRGT VCF allele lengths for this locus in sample A
  • b_AL TRGT VCF allele lengths for this locus in sample B
  • b_overlap_coverage Reciprocal of denovo_coverage, the number of reads in per allele in sample B that overlap compared to the sample A data