From FastQ data to high‐confidence variant calls: the genome analysis toolkit best practices pipeline

GA Van der Auwera, MO Carneiro… - Current protocols in …, 2013 - Wiley Online Library
GA Van der Auwera, MO Carneiro, C Hartl, R Poplin, G Del Angel, A Levy‐Moonshine…
Current protocols in bioinformatics, 2013Wiley Online Library
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.
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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