From FastQ Data to High‐Confidence Variant Calls: The Genome Analysis Toolkit Best Practices Pipeline. Issue 1 (15th March 2018)

• Record Type: Journal Article
• Authors: Van der Auwera, Geraldine A.; Carneiro, Mauricio O.; Hartl, Christopher; 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.
• Editors: Bateman, Alex; Pearson, William R.; Stein, Lincoln D.; Stormo, Gary D.; Yates, John R.
• Is Part Of: Current protocols in bioinformatics. Volume 43:Issue 1(2013)
• Page Start: 11.10.1
• Page End: 11.10.33
• Publication Date: 2018-03-15
• Subjects: NGS -- WGS -- exome -- variant detection -- genotyping; Bioinformatics -- Laboratory manuals; Nucleotide sequence -- Laboratory manuals; Amino acid sequence -- Laboratory manuals; Base Sequence; Amino Acid Sequence; Computational Biology -- methods; Databases, Genetic; Proteins -- analysis; Sequence Analysis -- methods; Sequence Homology; Amino acid sequence; Bioinformatics; Nucleotide sequence; Laboratory Manuals; Laboratory manuals; 570.285
• DOI: 10.1002/0471250953.bi1110s43
• Languages: English
• ISSNs: 1934-3396

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.