Tag: Genomics

In this blog post, we’ll show how you can run NVIDIA Parabricks on AWS Batch leveraging AWS CloudFormation templates. Parabricks is a GPU-accelerated tool for secondary genomic analysis. It reduces the runtime of variant calling on a 30x human genome from 30 hours to just 30 minutes, and leverages AWS Batch to provide an interface that scales compute jobs across multiple instances in the cloud.

Somatic variants are genetic alterations which are not inherited but acquired during one’s lifespan, for example those that are present in cancer tumors. In this post, we will demonstrate how to perform somatic variant calling from matched tumor and normal genome sequence data, as well as tumor-only whole genome and whole exome datasets using an NVIDIA GPU-accelerated Parabricks pipeline, and compare the results with baseline CPU-based workflows.

This blog provides an overview of NVIDIA’s Clara Parabricks along with a guide on how to use Parabricks within the AWS Marketplace. It focuses on germline analysis for whole genome and whole exome applications using GPU accelerated bwa-mem and GATK’s HaplotypeCaller.