UNIT 11.10 From FastQ Data to High-Confidence Variant Calls: The Genome Analysis Toolkit Best Practices Pipeline

  1. Geraldine A. Van der Auwera1,
  2. Mauricio O. Carneiro1,
  3. Christopher Hartl1,
  4. Ryan Poplin1,
  5. Guillermo del Angel1,
  6. Ami Levy-Moonshine1,
  7. Tadeusz Jordan1,
  8. Khalid Shakir1,
  9. David Roazen1,
  10. Joel Thibault1,
  11. Eric Banks1,
  12. Kiran V. Garimella2,
  13. David Altshuler1,
  14. Stacey Gabriel1,
  15. Mark A. DePristo1

Published Online: 15 OCT 2013

DOI: 10.1002/0471250953.bi1110s43

Current Protocols in Bioinformatics

Current Protocols in Bioinformatics

How to Cite

Van der Auwera, G. A., Carneiro, M. O., Hartl, C., Poplin, R., del Angel, G., Levy-Moonshine, A., Jordan, T., Shakir, K., Roazen, D., Thibault, J., Banks, E., Garimella, K. V., Altshuler, D., Gabriel, S. and DePristo, M. A. 2013. From FastQ Data to High-Confidence Variant Calls: The Genome Analysis Toolkit Best Practices Pipeline. Current Protocols in Bioinformatics. 11:11.10:11.10.1–11.10.33.

Author Information

  1. 1

    Genome Sequencing and Analysis Group, Broad Institute, Cambridge, Massachusetts

  2. 2

    Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom

Publication History

  1. Published Online: 15 OCT 2013


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.


  • NGS;
  • WGS;
  • exome;
  • variant detection;
  • genotyping