Helena Bioinformatics

Helena Bioinformatics Qc API

The qc API from Helena Bioinformatics — 2 operation(s) for qc.

GitHub OpenAPI

Operations 2

POST /sessions/{session_id}/qc Run QC checks #
GET /sessions/{session_id}/qc/variant-metrics Descriptive QC of stored variant records #

Specifications

⚙
OpenAPI
https://artifacts.apis.io/helena-bio/openapi/helena-bio-qc-api-openapi.yml

Schemas & Data

📊
JSONSchema
https://artifacts.apis.io/helena-bio/json-schema/helena-bio-mtdna-curation-fields-schema.json
📊
JSONSchema
https://artifacts.apis.io/helena-bio/json-schema/helena-bio-section-response-schema.json
📊
JSONSchema
https://artifacts.apis.io/helena-bio/json-schema/helena-bio-clin-var-lite-export-request-schema.json
📊
JSONSchema
https://artifacts.apis.io/helena-bio/json-schema/helena-bio-gene-literature-response-schema.json
📊
JSONSchema
https://artifacts.apis.io/helena-bio/json-schema/helena-bio-reclassification-run-detail-schema-schema.json
📊
JSONSchema
https://artifacts.apis.io/helena-bio/json-schema/helena-bio-vep-cache-stats-response-schema.json

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OpenAPI Specification

helena-bio-qc-api-openapi.yml Raw ↑ 
openapi: 3.2.0
info:
  title: Helix Insight - Variant Analysis Service Qc API
  description: AI-powered variant analysis and interpretation service
  version: 0.1.0
tags:
- name: qc
paths:
  /sessions/{session_id}/qc:
    post:
      tags:
      - qc
      summary: Run QC checks
      description: Run quality control checks on analysis session
      operationId: run_qc_checks_sessions__session_id__qc_post
      parameters:
      - name: session_id
        in: path
        required: true
        schema:
          type: string
          format: uuid
          title: Session Id
      requestBody:
        required: true
        content:
          application/json:
            schema:
              $ref: '#/components/schemas/QCCheckRequest'
      responses:
        '200':
          description: Successful Response
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/QCMetricsResponse'
        '422':
          description: Validation Error
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/HTTPValidationError'
  /sessions/{session_id}/qc/variant-metrics:
    get:
      tags:
      - qc
      summary: Descriptive QC of stored variant records
      operationId: get_variant_metrics_sessions__session_id__qc_variant_metrics_get
      security:
      - HTTPBearer: []
      parameters:
      - name: session_id
        in: path
        required: true
        schema:
          type: string
          format: uuid
          title: Session Id
      responses:
        '200':
          description: Successful Response
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/VariantQCResponse'
        '422':
          description: Validation Error
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/HTTPValidationError'
components:
  schemas:
    QCCheckRequest:
      properties:
        analysis_type:
          type: string
          title: Analysis Type
          description: 'Analysis type: wgs or wes'
      type: object
      required:
      - analysis_type
      title: QCCheckRequest
      description: Request schema for running QC checks.
      example:
        analysis_type: wgs
    VariantQCMetrics:
      properties:
        total_records:
          type: integer
          title: Total Records
        snv_count:
          anyOf:
          - type: integer
          - type: 'null'
          title: Snv Count
        transitions:
          anyOf:
          - type: integer
          - type: 'null'
          title: Transitions
        transversions:
          anyOf:
          - type: integer
          - type: 'null'
          title: Transversions
        ti_tv_ratio:
          anyOf:
          - type: number
          - type: 'null'
          title: Ti Tv Ratio
        depth_record_count:
          anyOf:
          - type: integer
          - type: 'null'
          title: Depth Record Count
        median_depth:
          anyOf:
          - type: number
          - type: 'null'
          title: Median Depth
        depth_ge_20_count:
          anyOf:
          - type: integer
          - type: 'null'
          title: Depth Ge 20 Count
        pct_variant_records_ge_20x:
          anyOf:
          - type: number
          - type: 'null'
          title: Pct Variant Records Ge 20X
        het_ab_record_count:
          anyOf:
          - type: integer
          - type: 'null'
          title: Het Ab Record Count
        het_ab_mean:
          anyOf:
          - type: number
          - type: 'null'
          title: Het Ab Mean
        het_ab_median:
          anyOf:
          - type: number
          - type: 'null'
          title: Het Ab Median
        mean_depth:
          anyOf:
          - type: number
          - type: 'null'
          title: Mean Depth
        depth_ge_10_count:
          anyOf:
          - type: integer
          - type: 'null'
          title: Depth Ge 10 Count
        pct_variant_records_ge_10x:
          anyOf:
          - type: number
          - type: 'null'
          title: Pct Variant Records Ge 10X
        diploid_genotype_count:
          anyOf:
          - type: integer
          - type: 'null'
          title: Diploid Genotype Count
        heterozygous_count:
          anyOf:
          - type: integer
          - type: 'null'
          title: Heterozygous Count
        homozygous_alt_count:
          anyOf:
          - type: integer
          - type: 'null'
          title: Homozygous Alt Count
        het_hom_alt_ratio:
          anyOf:
          - type: number
          - type: 'null'
          title: Het Hom Alt Ratio
        filter_record_count:
          anyOf:
          - type: integer
          - type: 'null'
          title: Filter Record Count
        pass_filter_count:
          anyOf:
          - type: integer
          - type: 'null'
          title: Pass Filter Count
        failed_filter_count:
          anyOf:
          - type: integer
          - type: 'null'
          title: Failed Filter Count
        not_applied_filter_count:
          anyOf:
          - type: integer
          - type: 'null'
          title: Not Applied Filter Count
        unknown_filter_count:
          anyOf:
          - type: integer
          - type: 'null'
          title: Unknown Filter Count
        pct_pass_filter:
          anyOf:
          - type: number
          - type: 'null'
          title: Pct Pass Filter
        computed_at:
          type: string
          title: Computed At
      type: object
      required:
      - total_records
      - snv_count
      - transitions
      - transversions
      - ti_tv_ratio
      - depth_record_count
      - mean_depth
      - depth_ge_10_count
      - pct_variant_records_ge_10x
      - diploid_genotype_count
      - heterozygous_count
      - homozygous_alt_count
      - het_hom_alt_ratio
      - filter_record_count
      - pass_filter_count
      - failed_filter_count
      - not_applied_filter_count
      - unknown_filter_count
      - pct_pass_filter
      - computed_at
      title: VariantQCMetrics
    VariantQCResponse:
      properties:
        session_id:
          type: string
          title: Session Id
        available:
          type: boolean
          title: Available
        reason:
          anyOf:
          - type: string
          - type: 'null'
          title: Reason
        scope:
          type: string
          const: stored_variant_records
          title: Scope
        schema_version:
          type: integer
          const: 1
          title: Schema Version
        single_sample:
          type: boolean
          title: Single Sample
        thresholds_applied:
          type: boolean
          const: false
          title: Thresholds Applied
        sample_metrics_reason:
          anyOf:
          - type: string
          - type: 'null'
          title: Sample Metrics Reason
        metrics:
          anyOf:
          - $ref: '#/components/schemas/VariantQCMetrics'
          - type: 'null'
      type: object
      required:
      - session_id
      - available
      - reason
      - scope
      - schema_version
      - single_sample
      - thresholds_applied
      - sample_metrics_reason
      - metrics
      title: VariantQCResponse
    HTTPValidationError:
      properties:
        detail:
          items:
            $ref: '#/components/schemas/ValidationError'
          type: array
          title: Detail
      type: object
      title: HTTPValidationError
    QCMetricsResponse:
      properties:
        session_id:
          type: string
          title: Session Id
        total_variants:
          type: integer
          title: Total Variants
        ti_tv_ratio:
          type: number
          title: Ti Tv Ratio
        het_hom_ratio:
          type: number
          title: Het Hom Ratio
        mean_depth:
          type: number
          title: Mean Depth
        pct_bases_above_10x:
          type: number
          title: Pct Bases Above 10X
        qc_passed:
          type: boolean
          title: Qc Passed
        failure_reasons:
          items:
            type: string
          type: array
          title: Failure Reasons
      type: object
      required:
      - session_id
      - total_variants
      - ti_tv_ratio
      - het_hom_ratio
      - mean_depth
      - pct_bases_above_10x
      - qc_passed
      - failure_reasons
      title: QCMetricsResponse
      description: Response schema for QC metrics.
    ValidationError:
      properties:
        loc:
          items:
            anyOf:
            - type: string
            - type: integer
          type: array
          title: Location
        msg:
          type: string
          title: Message
        type:
          type: string
          title: Error Type
        input:
          title: Input
        ctx:
          type: object
          title: Context
      type: object
      required:
      - loc
      - msg
      - type
      title: ValidationError
  securitySchemes:
    HTTPBearer:
      type: http
      scheme: bearer