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 inCurrent 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
LanguageEnglish
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
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Summary: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.
ISSN:1934-340X
DOI:10.1002/0471250953.bi1110s43