文献_2013-GATK3-UNIT 11.10 From FastQ Data to High-Confidence Variant Calls-The Genome Analysis Toolkit Best Practices Pipeline.pdf

From FastQ Data to High-Confidence UNIT 11.10 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 and Mark A. DePristo1 1Genome Sequencing and Analysis Group, Broad Institute, Cambridge, Massachusetts 2Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom 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. C Protoc. Bioinform. 43:11.10.1-11.10.33. 2013 by John Wiley Sons, Inc. Keywords: NGS WGS exome variant detection genotyping INTRODUCTION Genomic variant discovery seems like a fairly simple problem in principle—take reads mapped to a reference sequence, and, at every position, count the mismatches and deduce the genotype. In practice, it is made more complicated by multiple sources of error: amplification biases when the sample libraries are prepped in the wet lab, machine errors when the libraries are sequenced, software errors, and mapping artifacts when the reads are aligned. A good variant-calling workflow must involve data-preparation methods that correct or compensate for these various error modes. Variant discovery can then be performed on the appropriately processed data, using a robust calling algorithm that l