capabilities.work

Import Variants

A 3-step recipe with Amazon HealthOmics. We can help you get access.

Recipe · 3 steps

Import Variants

with Amazon HealthOmics

Create a variant store then import variants and wait for completion.

  1. Create a variant store bound to the supplied genome reference.
  2. Start a variant import job that loads the VCF items into the new store.
  3. Poll the variant import job until it reaches a terminal status. The status enum is SUBMITTED, IN_PROGRESS, CANCELLED, COMPLETED, FAILED, or COMPLETED_WITH_FAILURES.
What you'll need to have ready
  • storeName: A name for the new variant store (lowercase, starts with a letter).
  • referenceArn: The genome reference ARN the store is bound to.
  • roleArn: The service role ARN that HealthOmics assumes to read source files.
  • items: The variant import items, each with an S3 source URI.
For your developer

Arazzo workflow amazon-healthomics:import-variants, 3 operations: CreateVariantStore → StartVariantImportJob → GetVariantImportJob. Specs on APIs.io.

More recipes with Amazon HealthOmics

Activate an Archived Read SetExport a Read Set to S3Import AnnotationsImport Read SetImport Reference GenomeInspect a Run TaskProvision Genomics StoresRun a PrivateRun a Workflow in a Run Group