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From FastQ data to high confidence variant calls: the Genome Analysis Toolkit best practices pipeline
Open accessAbstract
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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“The best practices recommended by the Broad Institute for variant calling were then followed (Van der Auwera et al., 2013).”
From Loss of epigenetic information as a cause of mammalian aging (2023) · cites this paper as Van der Auwera et al., 2013
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Metadata
- 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
- 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
- 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
- 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
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
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