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05_OutputJsonFiles.md

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JSON files output by Expansion Hunter

JSON files generated by Expansion Hunter contain information about sample parameters (SampleParameters field) and analysis results summarized by locus (LocusResults field). The locus results contain these fields

  • AlleleCount The expected number of alleles at the locus
  • Coverage Estimated read coverage at the locus
  • FragmentLength The fragment size estimated from read pairs fully contained in either the left or right flank of the repeat region
  • LocusId Locus identifier
  • ReadLength Mean read length at the locus
  • Variants Genotypes and other information describing each variant analyzed at the locus

The structure of records in the Variant field is different for repeats and small variants (insertions, deletions, and swaps).

Repeat records

Repeat records contain the following fields.

  • VariantId Unique variant identifier
  • RepeatUnit Repeat unit in the reference orientation
  • VariantType Always set to "Repeat"
  • VariantSubtype Either "Repeat" or "RareRepeat"
  • Genotype Repeat genotype given by the size of each repeat allele
  • GenotypeConfidenceInterval Size confidence interval for each repeat allele
  • CountsOfSpanningReads Summary of identified spanning reads given as an array with entries (n, m) where n is the number of repeat units spanned by the flanking read and m is the number of such reads
  • CountsOfFlankingReads An analog of CountsOfSpanningReads for in-repeat reads
  • CountsOfInrepeatReads An analog of CountsOfSpanningReads for spanning reads
  • ReferenceRegion 0-based half-open reference coordinates of the repeat region (chrom:start-end)

Small variant records

Records for small variants contain the following fields.

  • VariantId Unique variant identifier
  • VariantType Always set to "SmallVariant"
  • VariantSubtype Either "Insertion", "Deletion", or "Swap"
  • RepeatUnit Repeat unit in the reference orientation
  • Genotype Formed, as usual, from 0s and 1s corresponding to ref and alt alleles
  • CountOfAltReads Number of reads supporting the alt allele
  • CountOfRefReads Number of reads supporting the ref allele
  • ReferenceRegion Reference region of the variant