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. 2020 Apr 23;11(4):460. doi: 10.3390/genes11040460

Table 3.

Exomiser analysis YML files (.yml) using different settings. Bold stands for analysis setting names and italics for functions.

Analysis YML File
1. DEFAULT
analysis:
  genomeAssembly: hg19
  vcf: path-to-VCF-file
  hpoIds: [comma-separated-list-of-HPO-terms]
  inheritanceModes: {
      AUTOSOMAL_DOMINANT: 0.1,
      AUTOSOMAL_RECESSIVE_HOM_ALT: 0.5,
      AUTOSOMAL_RECESSIVE_COMP_HET: 2.0,
      X_DOMINANT: 0.1,
      X_RECESSIVE_HOM_ALT: 0.5,
      X_RECESSIVE_COMP_HET: 2.0,
  }
  analysisMode: PASS_ONLY
  frequencySources: [LOCAL, THOUSAND_GENOMES, TOPMED, UK10K, ESP_AFRICAN_AMERICAN, ESP_EUROPEAN_AMERICAN, ESP_ALL, EXAC_AFRICAN_INC_AFRICAN_AMERICAN, EXAC_AMERICAN, EXAC_SOUTH_ASIAN, EXAC_EAST_ASIAN, EXAC_FINNISH, EXAC_NON_FINNISH_EUROPEAN, EXAC_OTHER, GNOMAD_E_AFR, GNOMAD_E_AMR, GNOMAD_E_EAS, GNOMAD_E_FIN, GNOMAD_E_NFE, GNOMAD_E_OTH, GNOMAD_E_SAS, GNOMAD_G_AFR, GNOMAD_G_AMR, GNOMAD_G_EAS, GNOMAD_G_FIN, GNOMAD_G_NFE, GNOMAD_G_OTH, GNOMAD_G_SAS]
  pathogenicitySources: [POLYPHEN, MUTATION_TASTER, SIFT]
  steps: [
      qualityFilter: {minQuality: 30.0}
      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_EXON_VARIANT, UPSTREAM_GENE_VARIANT, INTERGENIC_VARIANT, REGULATORY_REGION_VARIANT, CODING_TRANSCRIPT_INTRON_VARIANT, NON_CODING_TRANSCRIPT_INTRON_VARIANT, DOWNSTREAM_GENE_VARIANT]
      },
      frequencyFilter: {maxFrequency: 2.0},
      pathogenicityFilter: {keepNonPathogenic: true},
      inheritanceFilter: {},
      omimPrioritiser: {},
      hiPhivePrioritiser: {}
  ]		 2. VAR-ONLY
As per DEFAULT, but without
omimPrioritiser: {} and hiPhivePrioritiser: {}
3. CADD
As per DEFAULT, but with
pathogenicitySources: [CADD]
4. REVEL
As per DEFAULT, but with
pathogenicitySources: [REVEL]
5. MPC
As per DEFAULT, but with
pathogenicitySources: [MPC]
6. M_CAP
As per DEFAULT, but with
pathogenicitySources: [M_CAP]
7. MVP
As per DEFAULT, but with
pathogenicitySources: [MVP]
8. PRIMATE-AI
As per DEFAULT, but with
pathogenicitySources: [PRIMATE-AI]

LOCAL is University College London exome database (UCLex) [74]. Ensembl transcript annotation was used across all the analysis settings.