Cited by 6,687Genomics and Phylogenetic StudiesGenomics and Rare DiseasesGenetics, Bioinformatics, and Biomedical Research

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From FastQ data to high confidence variant calls: the Genome Analysis Toolkit best practices pipeline

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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.·2013·Current Protocols in Bioinformatics

DOI 10.1002/0471250953.bi1110s43PMC PMC4243306

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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.

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Authors: 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., & DePristo, M. A.
Affiliations: Genome Sequencing and Analysis Group Broad Institute Cambridge Massachusetts
Broad Institute (US)
Centre for Human Genetics (GB)
ORCID: Hartl, Christopher
Banks, Eric
Garimella, Kiran V.
Altshuler, David
Gabriel, Stacey
DePristo, Mark A.
Venue: Current Protocols in Bioinformatics
Publisher: Wiley
Published: 2013-10
Volume: 43
Issue: 1
Pages: 11.10.1-11.10.33
ISSN: 1934-3396 (ISSN-L)
1934-340X
DOI: 10.1002/0471250953.bi1110s43
PMC: PMC4243306
OpenAlex: W1919257374
Cited by: 6,687
References: 14
Citations by year: 2026: 342 · 2025: 559 · 2024: 677 · 2023: 662 · 2022: 729 · 2021: 877 · 2020: 716 · 2019: 648 · 2018: 528 · 2017: 416 · 2016: 293 · 2015: 168 · 2014: 60 · 2013: 2
FWCI: 78.15
Type: journal article
Language: en
Open access: green
www.ncbi.nlm.nih.gov
Licence: onlinelibrary.wiley.com/termsAndConditions#vor (vor, 1626 d)
Locations: Current Protocols in Bioinformatics (publishedVersion)
PubMed (publishedVersion)
Europe PMC (PubMed Central) (acceptedVersion)
PubMed Central (acceptedVersion)
Funders: National Human Genome Research Institute (U54HG003067, U01HG006569)
Topics: Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genomics and Rare Diseases
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genetics, Bioinformatics, and Biomedical Research
Keywords: variant calling, GATK, BWA, genome alignment, next-generation sequencing data processing, variant discovery, reference genome mapping, bioinformatics pipeline
MeSH terms: Calibration, Haploidy, Haplotypes, Humans, Software, Genetic Variation, Genome, Human, Sequence Alignment, Polymorphism, Single Nucleotide, Databases, Genetic, Molecular Sequence Annotation

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From FastQ data to high confidence variant calls: the Genome Analysis Toolkit best practices pipeline

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