From FastQ data to high confidence variant calls: the Genome Analysis Toolkit best practices pipeline.
Curr Protoc Bioinformatics
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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. |
Year of Publication | 2013
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Journal | Curr Protoc Bioinformatics
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Volume | 43
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Pages | 11.10.1-33
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Date Published | 2013
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ISSN | 1934-340X
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URL | |
DOI | 10.1002/0471250953.bi1110s43
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PubMed ID | 25431634
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PubMed Central ID | PMC4243306
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Grant list | U01 HG006569 / HG / NHGRI NIH HHS / United States
U54 HG003067 / HG / NHGRI NIH HHS / United States
U01HG006569 / HG / NHGRI NIH HHS / United States
U54HG003067 / HG / NHGRI NIH HHS / United States
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