Article
From FastQ data to high confidence variant calls: the Genome Analysis Toolkit best practices pipeline.
Current protocols in bioinformatics - 1 Jan 2013
Van der Auwera Geraldine A, Carneiro Mauricio O, Hartl Christopher, Poplin Ryan, Del Angel Guillermo, Levy-Moonshine Ami, Jordan Tadeusz, Shakir Khalid, Roazen David, Thibault Joel, Banks Eric, Garimella Kiran V, Altshuler David, Gabriel Stacey, DePristo Mark A
Abstract excerpt
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.
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