GATK

Description

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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

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