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. GATK aims to work well with both samtools and Picard by providing complementary tools. GATK SNP calling pipeline (Q score recalibration -> multiple sequence realignment -> snp/index calling) is a particular area of focus. Note: We provide a GenomeAnalysisTK wrapper script that calls java with the correct jar file, so you can call GATK with "GenomeAnalysisTK -T analysis_type [options] ...".

Environment Modules

Run module spider gatk to find out what environment modules are available for this application.

Environment Variables

• HPC_GATK_DIR - installation directory
• HPC_GATK_DOC - guide book directory

Categories

biology, ngs