Current Protocols in Bioinformatics

Volume 43, Issue 1 p. 11.10.1-11.10.33

UNIT

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

Geraldine A. Van der Auwera,

Geraldine A. Van der Auwera

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

Search for more papers by this author

Mauricio O. Carneiro,

Mauricio O. Carneiro

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

Search for more papers by this author

Christopher Hartl,

Christopher Hartl

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

Search for more papers by this author

Ryan Poplin,

Ryan Poplin

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

Search for more papers by this author

Guillermo del Angel,

Guillermo del Angel

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

Search for more papers by this author

Ami Levy-Moonshine,

Ami Levy-Moonshine

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

Search for more papers by this author

Tadeusz Jordan,

Tadeusz Jordan

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

Search for more papers by this author

Khalid Shakir,

Khalid Shakir

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

Search for more papers by this author

David Roazen,

David Roazen

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

Search for more papers by this author

Joel Thibault,

Joel Thibault

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

Search for more papers by this author

Eric Banks,

Eric Banks

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

Search for more papers by this author

Kiran V. Garimella,

Kiran V. Garimella

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

Search for more papers by this author

David Altshuler,

David Altshuler

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

Search for more papers by this author

Stacey Gabriel,

Stacey Gabriel

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

Search for more papers by this author

Mark A. DePristo,

Mark A. DePristo

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

Search for more papers by this author

Geraldine A. Van der Auwera,

Geraldine A. Van der Auwera

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

Search for more papers by this author

Mauricio O. Carneiro,

Mauricio O. Carneiro

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

Search for more papers by this author

Christopher Hartl,

Christopher Hartl

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

Search for more papers by this author

Ryan Poplin,

Ryan Poplin

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

Search for more papers by this author

Guillermo del Angel,

Guillermo del Angel

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

Search for more papers by this author

Ami Levy-Moonshine,

Ami Levy-Moonshine

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

Search for more papers by this author

Tadeusz Jordan,

Tadeusz Jordan

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

Search for more papers by this author

Khalid Shakir,

Khalid Shakir

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

Search for more papers by this author

David Roazen,

David Roazen

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

Search for more papers by this author

Joel Thibault,

Joel Thibault

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

Search for more papers by this author

Eric Banks,

Eric Banks

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

Search for more papers by this author

Kiran V. Garimella,

Kiran V. Garimella

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

Search for more papers by this author

David Altshuler,

David Altshuler

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

Search for more papers by this author

Stacey Gabriel,

Stacey Gabriel

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

Search for more papers by this author

Mark A. DePristo,

Mark A. DePristo

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

Search for more papers by this author

First published: 15 March 2018

https://doi.org/10.1002/0471250953.bi1110s43

Citations: 3,181

Read the full text

About

PDF

Tools

Share a link

Email
Facebook
Twitter
LinkedIn
Reddit
Wechat

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. Protoc. Bioinform. 43:11.10.1-11.10.33. © 2013 by John Wiley & Sons, Inc.

Literature Cited

1000 Genomes Project Consortium. 2010. A map of human genome variation from population-scale sequencing. Nature 467: 1061-1073.
10.1038/nature09534
CASPubMedWeb of Science®Google Scholar
DePristo, M.A., Banks, E., Poplin, R., Garimella, K.V., Maguire, J.R., Hartl, C., Philippakis, A.A., del Angel, G., Rivas, M.A., Hanna, M., McKenna, A., Fennell, T.J., Kernytsky, A.M., Sivachenko, A.Y., Cibulskis, K., Gabriel, S.B., Altshuler, D., and Daly, M.J. 2011. A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nat. Genet. 43: 491-498.
10.1038/ng.806
CASPubMedWeb of Science®Google Scholar
Fisher, R.A. 1922. On the interpretation of c² from contingency tables, and the calculation of p. J. R. Stat. Soc. 85: 87-94.
10.1111/j.2397-2335.1922.tb00768.x
Web of Science®Google Scholar
International HapMap 3 Consortium, Altshuler, D.M., Gibbs, R.A., Peltonen, L., Altshuler, D.M., Gibbs, R.A., Peltonen, L., Dermitzakis, E., Schaffner, S.F., Yu, F., Chang, K., Hawes, A., Lewis, L.R., Ren, Y., Wheeler, D., Gibbs, R.A., Muzny, D.M., Barnes, C., Darvishi, K., Hurles, M., Korn, J.M., Kristiansson, K., Lee, C., McCarrol, S.A., Nemesh, J., Dermitzakis, E., Keinan, A., Montgomery, S.B., Pollack, S., Price, A.L., 2Soranzo, N., Bonnen, P.E., Gibbs, R.A., Gonzaga-Jauregui, C., Keinan, A., Price, A.L., Yu, F., Anttila, V., Brodeur, W., Daly, M.J., Leslie, S., McVean, G., Moutsianas, L., Nguyen, H., Schaffner, S.F., Zhang, Q., Ghori, M.J., McGinnis, R., McLaren, W., Pollack, S., Price, A.L., Schaffner, S.F., Takeuchi, F., Grossman, S.R., Shlyakhter, I., Hostetter, E.B., Sabeti, P.C., Adebamowo, C.A., Foster, M.W., Gordon, D.R., Licinio, J., Manca, M.C., Marshall, P.A., Matsuda, I., Ngare, D., Wang, V.O., Reddy, D., Rotimi, C.N., Royal, C.D., Sharp, R.R., Zeng, C., Brooks, L.D., and McEwen, J.E. 2010. Integrating common and rare genetic variation in diverse human populations. Nature 467: 52-58.
10.1038/nature09298
CASPubMedWeb of Science®Google Scholar
Li, H. and Durbin, R. 2010. Fast and accurate long-read alignment with Burrows-Wheeler transform. Bioinformatics (Oxford) 26: 589-595.
10.1093/bioinformatics/btp698
CASPubMedWeb of Science®Google Scholar
Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N., Marth, G., Abecasis, G., and Durbin, R. 1000 Genome Project Data Processing Subgroup 2009. The Sequence Alignment/Map format and SAMtools. Bioinformatics (Oxford) 25: 2078-2079.
10.1093/bioinformatics/btp352
CASPubMedWeb of Science®Google Scholar
Mann, H.B. and Whitney, D.R. 1947. On a test of whether one of two random variables is stochastically larger than the other. Ann. Math. Stat. 18: 50-60.
10.1214/aoms/1177730491
Web of Science®Google Scholar
McKenna, A., Hanna, M., Banks, E., Sivachenko, A., Cibulskis, K., Kernytsky, A., Garimella, K., Altshuler, D., Gabriel, S., Daly, M., and DePristo, M.A. 2010. The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res. 20: 1297-1303.
10.1101/gr.107524.110
CASPubMedWeb of Science®Google Scholar
Mills, R.E., Luttig, C.T., Larkins, C.E., and Beauchamp, A. 2006. An initial map of insertion and deletion (INDEL) variation in the human genome. Genome Res. 16: 1182-1190.
10.1101/gr.4565806
CASPubMedWeb of Science®Google Scholar
Sherry, S.T., Ward, M.H., Kholodov, M., Baker, J., Phan, L., Smigielski, E.M., and Sirotkin, K. 2001. dbSNP: The NCBI database of genetic variation. Nucleic Acids Res. 29: 308-311.
10.1093/nar/29.1.308
CASPubMedWeb of Science®Google Scholar
Wickham, H. 2009. ggplot2: Elegant Graphics for Data Analysis. Springer, New York.
10.1007/978-0-387-98141-3
Web of Science®Google Scholar

Citing Literature

View the latest in Bioinformatics

This article also appears in:

Assembling and Mapping Large Sequence Sets

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

Abstract

Literature Cited

Citing Literature

References

Information

About Wiley Online Library

Help & Support

Opportunities

Connect with Wiley

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

Abstract

Literature Cited

Citing Literature

References

Related

Information