From fastQ data to high-confidence variant calls: The genome analysis toolkit best practices pipeline

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

Research output: Contribution to journalArticlepeer-review

4440 Scopus citations

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 dataprocessing 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.

Original languageEnglish
Article number11.10
JournalCurrent Protocols in Bioinformatics
Issue numberSUPL.43
DOIs
StatePublished - 1 Jan 2013
Externally publishedYes

Keywords

  • Exome
  • Genotyping
  • NGS
  • Variant detection
  • WGS

ASJC Scopus subject areas

  • Structural Biology
  • Biochemistry

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