title: From FastQ data to high confidence variant calls: the Genome Analysis Toolkit best practices pipeline.
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.
authors.affiliation: Genome Sequencing and Analysis Group, Broad Institute, Cambridge, Massachusetts.
authors.forename: Geraldine A
authors.initials: GA
authors.lastname: Van der Auwera
authors.affiliation: Genome Sequencing and Analysis Group, Broad Institute, Cambridge, Massachusetts.
authors.forename: Mauricio O
authors.initials: MO
authors.lastname: Carneiro
authors.affiliation: Genome Sequencing and Analysis Group, Broad Institute, Cambridge, Massachusetts.
authors.forename: Christopher
authors.initials: C
authors.lastname: Hartl
authors.affiliation: Genome Sequencing and Analysis Group, Broad Institute, Cambridge, Massachusetts.
authors.forename: Ryan
authors.initials: R
authors.lastname: Poplin
authors.affiliation: Genome Sequencing and Analysis Group, Broad Institute, Cambridge, Massachusetts.
authors.forename: Guillermo
authors.initials: G
authors.lastname: Del Angel
authors.affiliation: Genome Sequencing and Analysis Group, Broad Institute, Cambridge, Massachusetts.
authors.forename: Ami
authors.initials: A
authors.lastname: Levy-Moonshine
authors.affiliation: Genome Sequencing and Analysis Group, Broad Institute, Cambridge, Massachusetts.
authors.forename: Tadeusz
authors.initials: T
authors.lastname: Jordan
authors.affiliation: Genome Sequencing and Analysis Group, Broad Institute, Cambridge, Massachusetts.
authors.forename: Khalid
authors.initials: K
authors.lastname: Shakir
authors.affiliation: Genome Sequencing and Analysis Group, Broad Institute, Cambridge, Massachusetts.
authors.forename: David
authors.initials: D
authors.lastname: Roazen
authors.affiliation: Genome Sequencing and Analysis Group, Broad Institute, Cambridge, Massachusetts.
authors.forename: Joel
authors.initials: J
authors.lastname: Thibault
authors.affiliation: Genome Sequencing and Analysis Group, Broad Institute, Cambridge, Massachusetts.
authors.forename: Eric
authors.initials: E
authors.lastname: Banks
authors.affiliation: Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom.
authors.forename: Kiran V
authors.initials: KV
authors.lastname: Garimella
authors.affiliation: Genome Sequencing and Analysis Group, Broad Institute, Cambridge, Massachusetts.
authors.forename: David
authors.initials: D
authors.lastname: Altshuler
authors.affiliation: Genome Sequencing and Analysis Group, Broad Institute, Cambridge, Massachusetts.
authors.forename: Stacey
authors.initials: S
authors.lastname: Gabriel
authors.affiliation: Genome Sequencing and Analysis Group, Broad Institute, Cambridge, Massachusetts.
authors.forename: Mark A
authors.initials: MA
authors.lastname: DePristo
mesh_terms: D002138:Calibration; D030541:Databases, Genetic; D014644:Genetic Variation; D015894:Genome, Human; D006238:Haploidy; D006239:Haplotypes / Q000235:genetics; D006801:Humans; D058977:Molecular Sequence Annotation; D020641:Polymorphism, Single Nucleotide / Q000235:genetics; D016415:Sequence Alignment; D012984:Software
keywords: NGS; WGS; exome; genotyping; variant detection