1. Publications

From FastQ data to high confidence variant calls: the Genome Analysis Toolkit best practices pipeline

Geraldine A. Van der Auwera, Mauricio O. Carneiro, Chris Hartl, Ryan Poplin, Guillermo del Angel, Ami Levy-Moonshine, Tadeusz Jordan, Khalid Shakir, David Roazen, Joel Thibault, Eric Banks, Kiran V. Garimella,1 David Altshuler, Stacey Gabriel, and Mark A. DePristo.
Current protocols in bioinformatics. 2013; 
Abstract
This unit describes how to use BWA and the Genome Analysis Toolkit (GATK) to map genome sequencing data to a reference and produce high-quality variant calls that can be used in downstream analyses. The complete workflow includes the core NGS data-processing steps that are necessary to make the raw data suitable for analysis by the GATK, as well as the key methods involved in variant discovery using the GATK.