Orangenomix DeepVariant - Genomic Variant Calling on AWS Batch

Run Google's DeepVariant variant caller at scale across large genomic datasets without building or managing your own pipeline infrastructure. This product provides a fully orchestrated, fault-tolerant mechanism to deploy and execute DeepVariant over large collections of files using AWS-native services.

The pipeline follows a straightforward data flow designed for production genomic workloads:

• Data Ingestion from S3: Input files (BAM/CRAM and reference genomes) are consumed directly from your Amazon S3 buckets, eliminating the need for manual data transfers or staging.
• Processing via AWS Batch: DeepVariant jobs are submitted and executed through AWS Batch, which handles compute provisioning, job scheduling, and resource management automatically.
• Results Returned to S3: Variant call outputs (VCF/gVCF files) are written back to your designated S3 bucket, ready for downstream analysis or integration with other bioinformatics tools.

Scalability Through AWS Batch Process anywhere from a handful of samples to large population-scale cohorts. AWS Batch dynamically scales compute resources up or down based on your workload, so you only use what you need. Submit hundreds of jobs and let the architecture handle parallel execution across your dataset.

Built-In Fault Tolerance Production genomic pipelines cannot afford silent failures. This architecture includes automatic error detection, retry logic, and job-level fault tolerance. If a job fails due to a transient infrastructure issue, the system handles recovery without manual intervention. Errors are captured, logged, and reported so you maintain full visibility into every run.

Error Handling and Reporting Failed jobs are not lost or ignored. The pipeline tracks job status across your entire submission, surfaces errors with actionable detail, and ensures you know exactly which files succeeded and which require attention.

Simple Configuration Get started without extensive pipeline engineering. Configuration is designed to be straightforward, allowing you to point the pipeline at your S3 data and begin processing with minimal setup overhead.

This product is purpose-built for teams that need to run DeepVariant at production scale on AWS. Rather than spending weeks building custom orchestration around DeepVariant containers, configuring retry logic, managing job queues, and handling edge cases, you can leverage a pre-built architecture that addresses these operational concerns out of the box.

Typical workflows supported include:

• Germline variant calling across whole-genome sequencing (WGS) datasets
• Batch processing of large sample cohorts for research or clinical genomics programs
• Scalable reprocessing of archived sequencing data stored in S3

This product leverages core AWS services to deliver a cloud-native genomics pipeline:

• Amazon S3 for input and output data storage
• AWS Batch for managed compute orchestration and job scheduling
• Native AWS scaling to grow compute capacity based on workload demands

All processing stays within your AWS account, and data remains in your S3 buckets throughout the pipeline.

After subscribing, configure the pipeline to point at your S3 input data and begin submitting DeepVariant jobs through AWS Batch. The architecture handles compute provisioning, job execution, fault recovery, and result delivery back to S3.

For technical questions, deployment guidance, or to discuss your specific genomic workflow requirements, reach out to the Orangenomix team through the support channels provided on this listing.