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 dataprocessing 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.
Original language | English |
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Article number | 11.10 |
Journal | Current Protocols in Bioinformatics |
Issue number | SUPL.43 |
DOIs | |
State | Published - 1 Jan 2013 |
Externally published | Yes |
Keywords
- Exome
- Genotyping
- NGS
- Variant detection
- WGS
ASJC Scopus subject areas
- Structural Biology
- Biochemistry