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. 2013;43(1110):11.10.1-11.10.33.
doi: 10.1002/0471250953.bi1110s43.

From FastQ data to high confidence variant calls: the Genome Analysis Toolkit best practices pipeline

Geraldine A Van der Auwera  1 , Mauricio O Carneiro  1 , Christopher Hartl  1 , Ryan Poplin  1 , Guillermo Del Angel  1 , Ami Levy-Moonshine  1 , Tadeusz Jordan  1 , Khalid Shakir  1 , David Roazen  1 , Joel Thibault  1 , Eric Banks  1 , Kiran V Garimella  2 , David Altshuler  1 , Stacey Gabriel  1 , Mark A DePristo  1
Affiliations

From FastQ data to high confidence variant calls: the Genome Analysis Toolkit best practices pipeline

Geraldine A Van der Auwera et al. Curr Protoc Bioinformatics. 2013.

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.

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

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Figures

Figure 1
Figure 1
Strategic planning workflow for the protocols included in this unit.
See this image and copyright information in PMC

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