analysis:
  genomeAssembly: hg38
  vcf: temp//14777_exomiser.vcf
  ped: temp//14777_exomiser.ped
  proband: SAMPLEID
  hpoIds:
  - HP:0001250
  - HP:0001919
  - HP:0001254
  - HP:0001942
  - HP:0001998
  - HP:0002151
  - HP:0008872
  - HP:0008936
  - HP:0012751
  - HP:0012758
  - HP:0025045
  - HP:0033198
  - HP:0000001
  - HP:0000002
  - HP:0000003
  - HP:0000004
  - HP:0000005
  - HP:0003557
  - HP:0009077
  - HP:0002527
  - HP:0011717
  - HP:0003623
  - HP:0011968
  - HP:0001943
  - HP:0012377
  - HP:0012757
  - HP:0000194
  inheritanceModes:
    AUTOSOMAL_DOMINANT: 0.25
    AUTOSOMAL_RECESSIVE_COMP_HET: 1.0
    AUTOSOMAL_RECESSIVE_HOM_ALT: 0.5
    X_DOMINANT: 0.25
    X_RECESSIVE_COMP_HET: 1.0
    X_RECESSIVE_HOM_ALT: 1.0
    MITOCHONDRIAL: 1.0
  analysisMode: PASS_ONLY
  frequencySources:
  - TOPMED
  - GNOMAD_E_AFR
  - GNOMAD_E_AMR
  - GNOMAD_E_EAS
  - GNOMAD_E_NFE
  - GNOMAD_E_SAS
  - GNOMAD_G_AFR
  - GNOMAD_G_AMR
  - GNOMAD_G_EAS
  - GNOMAD_G_NFE
  - GNOMAD_G_SAS
  pathogenicitySources:
  - REVEL
  - MVP
  steps:
  - failedVariantFilter: {}
  - variantEffectFilter:
      remove:
      - FIVE_PRIME_UTR_EXON_VARIANT
      - FIVE_PRIME_UTR_INTRON_VARIANT
      - THREE_PRIME_UTR_EXON_VARIANT
      - THREE_PRIME_UTR_INTRON_VARIANT
      - NON_CODING_TRANSCRIPT_INTRON_VARIANT
      - CODING_TRANSCRIPT_INTRON_VARIANT
      - UPSTREAM_GENE_VARIANT
      - DOWNSTREAM_GENE_VARIANT
      - INTERGENIC_VARIANT
      - REGULATORY_REGION_VARIANT
  - hiPhivePrioritiser: {}
  - priorityScoreFilter:
      priorityType: HIPHIVE_PRIORITY
      minPriorityScore: 0.501
  - frequencyFilter:
      maxFrequency: 1.0
  - pathogenicityFilter:
      keepNonPathogenic: true
  - inheritanceFilter: {}
  - omimPrioritiser: {}
outputOptions:
  outputContributingVariantsOnly: false
  numGenes: 1000
  outputPrefix: temp//14777_exomiser
  outputFormats:
  - TSV_VARIANT
  - HTML
  - TSV_GENE