From FastQ Data to High‐Confidence Variant Calls: The Genome Analysis Toolkit Best Practices Pipeline

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.

Keywords

WorkflowComputer sciencePipeline (software)Key (lock)GenomeReference genomeRaw dataComputational biologyData miningBiologyDatabaseGeneticsGeneProgramming languageOperating system

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Publication Info

Year: 2013
Type: article
Volume: 43
Issue: 1
Pages: 11.10.1-11.10.33
Citations: 6905
Access: Closed

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APA Style

                            
                                
                                    Géraldine Van der Auwera, 
                                
                                    Mauricio O. Carneiro, 
                                
                                    Christopher Hartl
                                
                                et al.
                            
                            (2013). 
                            From FastQ Data to High‐Confidence Variant Calls: The Genome Analysis Toolkit Best Practices Pipeline. 
                            Current Protocols in Bioinformatics
                            , 43
                            (1)
                            , 11.10.1-11.10.33.
                            https://doi.org/10.1002/0471250953.bi1110s43
                        

Identifiers

DOI: 10.1002/0471250953.bi1110s43