GATK
Description
The GATK is a structured software library that makes writing efficient analysis tools using next-generation sequencing data very easy, and second it's a suite of tools for working with human medical resequencing projects such as 1000 Genomes and The Cancer Genome Atlas. These tools include things like a depth of coverage analyzers, a quality score recalibrator, a SNP/indel caller and a local realigner.
We aim to work well with both samtools and Picard by providing complementary tools to those available in those two packages. Our SNP calling pipeline (Q score recalibration -> multiple sequence realignment -> snp/index calling) is a particular area of focus, and have been pushing to make these capabilities as general-purpose and powerful as possible. My group's mandate is to ensure the success of the human medical resequencing projects we've undertaken at the Broad over the next 2-3 years, which involves providing a robust, production-quality development library that underlies tools for common analysis problems (like SNP calling) as well as enabling exploratory research on NGS data. Upstream documentation for gatk. Template:App Location
Available versions
- 1.4.30
- 1.6.9
Running the application using modules
To use gatk with the environment modules system at HPC the following commands are available:
Get module information for gatk:
$module spider gatk
Load the default application module:
$module load gatk
The modulefile for this software adds the directory with executable files to the shell execution PATH and sets the following environment variables:
- HPC_GATK_DIR - directory where gatk is located.
How To Run
We provide two wrapper scripts AnalyzeCovariates and GenomeAnalysisTK that are equivalent to running
java -jar $HPC_GATK_DIR/GenomeAnalysisTK.jar
and
java -jar $HPC_GATK_DIR/AnalyzeCovariates.jar