GATK

Description

gatk website  

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.

Execution Environment and 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