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API Reference

The AIVA API provides programmatic access to the platform's core features. Use it to automate file uploads, run variant calling pipelines, interact with the AI assistant, manage databases, classify variants, export annotations, and integrate with MCP-compatible clients.


Base URL

All API endpoints are relative to:

https://api.aivaportal.com

Authentication

All API requests require authentication using an API key. Include your API key in the Authorization header:

Authorization: Bearer <AIVA_API_KEY>

See API Keys for instructions on creating and managing API keys.


Endpoint Summary

Endpoint Method Path Description
Health Check GET /health Test API connection and verify key validity
FASTQ Upload POST /jobs/upload/parabricks Upload FASTQ files for variant calling
FASTQ Cloud Upload POST /jobs/upload/parabricks Upload FASTQ from cloud URLs
VCF Direct Upload POST /jobs/upload Upload VCF/CSV/TSV files directly
VCF Cloud Upload POST /jobs/upload/from-cloud-url Import VCF from cloud URL
VCF Annotated Upload POST /jobs/upload Upload VCF with Small Variant Annotation
VCF Annotated Cloud Upload POST /jobs/upload/from-cloud-url Import VCF from cloud with Small Variant Annotation
VCF SV Annotation Upload POST /jobs/upload Upload VCF with Structural Variant Annotation
VCF SV Annotation Cloud Upload POST /jobs/upload/from-cloud-url Import VCF from cloud with Structural Variant Annotation
Job Events (SSE) GET /jobs/events?token=<API_KEY> Real-time job status via SSE
Job Status GET /jobs/{job_id}/status Poll individual job status
List Jobs GET /jobs List all jobs
Cancel Job POST /jobs/{job_id}/cancel Cancel a running job
Delete Job DELETE /jobs/{job_id} Delete a job
AI Chat POST /agents/chat/stream Stream AI chat responses
Classify Variant POST /api/analyze/classify-variant ACMG/AMP variant classification
List Tables GET /tables List uploaded data tables
Get Table Data GET /tables/{table_name}/data/all Retrieve table data
Delete Table DELETE /tables/{table_name} Delete a table
Export Flags GET /api/variant-flags/export Export variant flags
Export Comments GET /api/variant-comments/export Export variant comments
MCP SSE GET /mcp/sse MCP integration endpoint

In This Section

API Keys

Create, manage, and revoke API keys. Verify connectivity with the health check endpoint.

API Keys

Upload Endpoints

Upload FASTQ, VCF, CSV, and TSV files directly or via cloud URLs, with optional Small Variant Annotation or Structural Variant Annotation.

Upload Endpoints

Job Monitoring

Monitor upload and processing jobs via SSE real-time events or polling.

Job Monitoring

Chat API

Interact with the AIVA AI assistant programmatically with streaming SSE responses.

Chat API

Classification API

Classify variants using ACMG or AMP guidelines with AI-powered analysis.

Classification API

Database Queries

List, retrieve, and delete your uploaded variant data tables.

Database Queries

Export API

Export variant flags and threaded comments in CSV format.

Export API

MCP Setup

Connect AIVA as an MCP server to Claude Desktop or other MCP-compatible clients.

MCP Setup


Error Handling

The API uses standard HTTP status codes:

Code Meaning
200 Success
201 Resource created
400 Bad request: check your parameters
401 Unauthorized: invalid or missing API key
403 Forbidden: insufficient permissions or subscription tier
404 Resource not found
429 Rate limit exceeded
500 Internal server error

Error responses include a JSON body:

{
  "detail": "Error message describing the issue."
}

Content Types

  • File upload requests use multipart/form-data.
  • JSON body requests use application/json.
  • Responses are application/json unless otherwise noted.
  • Streaming endpoints use text/event-stream (Server-Sent Events).