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

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...

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Bibliographic Details
Published in	Current protocols in bioinformatics Vol. 43; p. 11.10.1
Main Authors	Van der Auwera, Geraldine A, Carneiro, Mauricio O, Hartl, Chris, Poplin, Ryan, Del Angel, Guillermo, Levy-Moonshine, Ami, Jordan, Tadeusz, Shakir, Khalid, Roazen, David, Thibault, Joel, Banks, Eric, Garimella, Kiran V, Altshuler, David, Gabriel, Stacey, DePristo, Mark A
Format	Journal Article
Language	English
Published	United States 2013
Subjects	Calibration Databases, Genetic Genetic Variation Genome, Human Haploidy Haplotypes - genetics Humans Molecular Sequence Annotation Polymorphism, Single Nucleotide - genetics Sequence Alignment Software WGS exome NGS variant detection genotyping
Online Access	Get more information
ISSN	1934-340X
DOI	10.1002/0471250953.bi1110s43

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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.
AbstractList	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.
Author	Jordan, Tadeusz Roazen, David Del Angel, Guillermo Banks, Eric Gabriel, Stacey Carneiro, Mauricio O Garimella, Kiran V Hartl, Chris Van der Auwera, Geraldine A Thibault, Joel DePristo, Mark A Levy-Moonshine, Ami Poplin, Ryan Shakir, Khalid Altshuler, David
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BackLink	https://www.ncbi.nlm.nih.gov/pubmed/25431634$$D View this record in MEDLINE/PubMed
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References	20811451 - Nature. 2010 Sep 2;467(7311):52-8 19505943 - Bioinformatics. 2009 Aug 15;25(16):2078-9 20981092 - Nature. 2010 Oct 28;467(7319):1061-73 20080505 - Bioinformatics. 2010 Mar 1;26(5):589-95 20644199 - Genome Res. 2010 Sep;20(9):1297-303 21478889 - Nat Genet. 2011 May;43(5):491-8 16902084 - Genome Res. 2006 Sep;16(9):1182-90 11125122 - Nucleic Acids Res. 2001 Jan 1;29(1):308-11
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Title	From FastQ data to high confidence variant calls: the Genome Analysis Toolkit best practices pipeline
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