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Curr Protoc Bioinformatics. 2013;43:11.10.1-11.10.33. doi: 10.1002/0471250953.bi1110s43.

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

Author information

1
Genome Sequencing and Analysis Group, Broad Institute, Cambridge, Massachusetts.
2
Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom.

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.

KEYWORDS:

NGS; WGS; exome; genotyping; variant detection

PMID:
25431634
PMCID:
PMC4243306
DOI:
10.1002/0471250953.bi1110s43
[Indexed for MEDLINE]
Free PMC Article

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