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Curr Protoc Bioinformatics. 2013;43:11.10.1-33. doi: 10.1002/0471250953.bi1110s43.

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

Author information

1
Broad Institute, Genome Sequencing and Analysis Group, 301 Binney Street, Cambridge MA 02142.
2
Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK.

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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