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

互联网2013-12-31

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Abstract
Table of Contents
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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.

Keywords: NGS; WGS; exome; variant detection; genotyping

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Introduction
Strategic Planning
Basic Protocol 1: From FASTQ to Analysis‐Ready BAM: Preparing the Sequence Data
Basic Protocol 2: From Analysis‐Ready BAM to Raw Variants: Calling Variants in Diploid Organisms with HaplotypeCaller
Basic Protocol 3: From Raw to Analysis‐Ready Variants: Variant Quality Score Recalibration
Alternate Protocol 1: From Analysis‐Ready BAM to Raw Variants: Calling Variants in Non‐Diploid Organisms with UnifiedGenotyper
Alternate Protocol 2: From Raw to Analysis‐Ready Variants: Hard Filtering Small Datasets
Support Protocol 1: Obtaining and Installing the Software Used in This Unit
Support Protocol 2: From BAM Back to FASTQ: Reprocessing Old Data
Support Protocol 3: Fixing Improperly Formatted BAM Files
Support Protocol 4: Adding Variant Annotations with VariantAnnotator
Acknowledgments
Literature Cited
Figures

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Materials

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Figures

Figure 11.10.1 Strategic planning workflow for the protocols included in this unit.

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Literature Cited

Literature Cited
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