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

Curr Protoc Bioinformatics
Authors
Keywords
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
Journal
Curr Protoc Bioinformatics
Volume
43
Pages
11.10.1-33
Date Published
2013
ISSN
1934-340X
URL
DOI
10.1002/0471250953.bi1110s43
PubMed ID
25431634
PubMed Central ID
PMC4243306
Links
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