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

Artículo

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

Géraldine Van der Auwera; Mauricio O. Carneiro; Christopher Hartl; Ryan Poplin; Guillermo del Angel; Ami Levy‐Moonshine; Tadeusz Jordan; Khalid Shakir · Current Protocols in Bioinformatics · 2013

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Author / responsible party

Géraldine Van der Auwera; Mauricio O. Carneiro; Christopher Hartl; Ryan Poplin; Guillermo del Angel; Ami Levy‐Moonshine; Tadeusz Jordan; Khalid Shakir

Publisher

Current Protocols in Bioinformatics

Year

2013

Language

English

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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. Curr. Protoc. Bioinform . 43:11.10.1‐11.10.33. © 2013 by John Wiley & Sons, Inc.

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APA 7

Auwera, G. V. D, Carneiro, M. O, Hartl, C, Poplin, R, Angel, G. D, Levy‐Moonshine, A, Jordan, T, & Shakir, K. (2013). From FastQ Data to High‐Confidence Variant Calls: The Genome Analysis Toolkit Best Practices Pipeline. https://doi.org/10.1002/0471250953.bi1110s43

MLA

Auwera, Géraldine Van der, et al. "From FastQ Data to High‐Confidence Variant Calls: The Genome Analysis Toolkit Best Practices Pipeline." 2013. https://doi.org/10.1002/0471250953.bi1110s43.

Chicago

Auwera, Géraldine Van der, Mauricio O. Carneiro, Christopher Hartl, Ryan Poplin, Guillermo del Angel, Ami Levy‐Moonshine, Tadeusz Jordan, and Khalid Shakir. 2013. "From FastQ Data to High‐Confidence Variant Calls: The Genome Analysis Toolkit Best Practices Pipeline.". https://doi.org/10.1002/0471250953.bi1110s43.

Harvard

Auwera, G. V. D. et al. 2013, From FastQ Data to High‐Confidence Variant Calls: The Genome Analysis Toolkit Best Practices Pipeline, Current Protocols in Bioinformatics, available at: https://doi.org/10.1002/0471250953.bi1110s43 [Accessed 8 Aug. 2026].

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

Author / contributors: Géraldine Van der Auwera; Mauricio O. Carneiro; Christopher Hartl; Ryan Poplin; Guillermo del Angel; Ami Levy‐Moonshine; Tadeusz Jordan; Khalid Shakir

Publisher: Current Protocols in Bioinformatics

Publication year: 2013

Language: English

Subjects

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Workflow; Computer science; Pipeline (software); Key (lock); Genome; Reference genome; Raw data; Computational biology; Data mining; Biology; Database; Genetics