Infrastructure for GATK* Best Practices Pipeline Deployment

Infrastructure for GATK* Best Practices Pipeline Deployment

Infrastructure for GATK* Best Practices Pipeline Deployment

Overview
This document is a guide for the reference platform and benchmarking effort for the Broad Institute. The benchmarking effort involves automating the GATK* best practices pipeline from the Broad Institute (Broad) as well as provide system-level data for this pipeline to show how best to utilize the latest Intel® architecture-based platforms.

This pipeline implementation of the GA...TK best practices recommendations from the Broad is constructed as a Perl script along with BWA for alignment, and Picard Tools for sorting. In addition to running these tools, system-level data for the individual tools as well as the overall pipeline is gathered via Workflow Profiler, an Intel Open Source Project.

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