gnomad-ga4gh-api-testing.ipynb

gnomad_vrs_va.graphql

fragment VADefiniteRange on VADefiniteRange {
  type
  min
  max
}

fragment VAIndefiniteRange on VAIndefiniteRange {
  type
  indefinite_value: value
  comparator
}

fragment VANumber on VANumber {
  type
  value
}

fragment VASequenceLocation on VASequenceLocation {
  _id {
    value
  }
  type
  sequence_id
  interval {
    type
    start {
      ...VADefiniteRange
      ...VAIndefiniteRange
      ...VANumber
    }
    end {
      ...VADefiniteRange
      ...VAIndefiniteRange
      ...VANumber
    }
  }
}

fragment VACURIE on VACURIE {
  value
}

fragment VALiteralSequenceExpression on VALiteralSequenceExpression {
  type
  sequence
}

fragment VAAncillaryResults on VAAncillaryResults {
	grpMaxFAF95 {
    frequency
    confidenceInterval
    groupId
  }
  jointGrpMaxFAF95 {
    frequency
    confidenceInterval
    groupId
  }
  homozygotes
  hemizygotes
}

fragment VACohort on VACohort {
  id
  label
  characteristics {
    name
    value
  }
}

fragment VACohortAlleleFrequencyCommonFields on VACohortAlleleFrequency {
  id
  type
  label
  derivedFrom {
    id
    type
    label
    version
  }
  focusAllele {
    ... on VAAllele {
      _id {
        value
      }
      type
    }
    ... on VAFocusAlleleURI {
      value
    }
  }
  focusAlleleCount
  locusAlleleCount
  alleleFrequency
  cohort {
    ...VACohort
  }
  ancillaryResults {
    ...VAAncillaryResults
  }
}

fragment TopLevelVACohortAlleleFrequency on VACohortAlleleFrequency {
  ...VACohortAlleleFrequencyCommonFields
  subcohortFrequency {
    ...VACohortAlleleFrequencyCommonFields
    subcohortFrequency {
      ...VACohortAlleleFrequencyCommonFields
      # id
      # type
    }
  }
}

query gnomad_va($variantId: String!) {
  va(variantId: $variantId) {
    vrs {
      _id {
        value
      }
      type
      location {
        ...VASequenceLocation
        ...VACURIE
      }
      state {
        ...VALiteralSequenceExpression
      }
    }
    va {
      ...TopLevelVACohortAlleleFrequency
    }
  }
}