The IAAP Genotyping Orchestrated Worfklow is a fully orchestrated workflow that takes a set of raw intensity data, a bead pool manifest, and cluster files as input, and reports genotype calls along with sample-level quality metrics in various formats such as Illumina GTC format and PED Files. It uses a set of public, secure APIs to facilitate its integration with an upstream or downstream pipeline. The Genotyping Orchestrated Workflow is able to manage the orchestration of samples across different worker nodes and can be scaled up or down to tailor the compute power to your sample throughput.
Illumina Array Analysis Platform Genotyping Command Line Interface
The IAAP Genotyping Command Line Interface (CLI) allows you to integrate the Genotyping workflow into an existing, fully-orchestrated data analysis pipeline. The CLI provides the same core functionality as the IAAP Genotyping Orchestrated Workflow but does not manage samples through the workflow or depend on Docker.