From FastQ Data to High‐Confidence Variant Calls: The Genome Analysis Toolkit Best Practices Pipeline
Géraldine Van der Auwera(Broad Institute), Mauricio O. Carneiro(Broad Institute), Christopher Hartl(Broad Institute), Ryan Poplin(Broad Institute), Guillermo del Angel(Broad Institute), Ami Levy‐Moonshine(Broad Institute), Tadeusz Jordan(Broad Institute), Khalid Shakir(Broad Institute), David Roazen(Broad Institute), Joel Thibault(Broad Institute), Eric Banks(Broad Institute), Kiran Garimella(Centre for Human Genetics), David Altshuler(Broad Institute), Stacey Gabriel(Broad Institute), Mark A. DePristo(Broad Institute)
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Abstract
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. Curr. Protoc. Bioinform . 43:11.10.1‐11.10.33. © 2013 by John Wiley & Sons, Inc.
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