GATK

Software Summary

Mesabi

Default Module: 

4.1.2

Other Modules Available: 

3.7.0, 4.1.2, 4.0.11, 4.0.6, 3.3.0, 3.1.1, 3.2.2, 3.4.0, 3.5.0, 3.6.0, 1.6, 3.2.0, 2.7.2

Last Updated On: 

Tuesday, March 8, 2022

Mesabi K40

Default Module: 

4.1.2
Other Modules Available: 

3.7.0, 4.1.2, 4.0.11, 4.0.6, 3.3.0, 3.1.1, 3.2.2, 3.4.0, 3.5.0, 3.6.0, 1.6, 3.2.0, 2.7.2

Last Updated On: 

Tuesday, March 8, 2022

Mangi

Default Module: 
4.1.2
Other Modules Available: 

3.7.0, 4.1.2, 4.0.11, 4.0.6, 3.3.0, 3.1.1, 3.2.2, 3.4.0, 3.5.0, 3.6.0, 1.6, 3.2.0, 2.7.2

Last Updated On: 

Tuesday, March 8, 2022

Mangi v100

Default Module: 

4.1.2
Other Modules Available: 

3.7.0, 4.1.2, 4.0.11, 4.0.6, 3.3.0, 3.1.1, 3.2.2, 3.4.0, 3.5.0, 3.6.0, 1.6, 3.2.0, 2.7.2

Last Updated On: 

Tuesday, March 8, 2022

NICE

Default Module: 

4.1.2

Other Versions Available: 

3.7.0, 4.1.2, 4.0.11, 4.0.6, 3.3.0, 3.1.1, 3.2.2, 3.4.0, 3.5.0, 3.6.0, 1.6, 3.2.0, 2.7.2

Last Updated On: 

Tuesday, March 8, 2022

Last Updated On: 

Tuesday, March 8, 2022

Support Level: 
Primary Support
Software Access Level: 
Open Access
Software Categories: 
Genetics
Software Description

From the GATK website:

A genomic analysis toolkit focused on variant discovery.

The GATK is the industry standard for identifying SNPs and indels in germline DNA and RNAseq data. Its scope is now expanding to include somatic short variant calling, and to tackle copy number (CNV) and structural variation (SV). In addition to the variant callers themselves, the GATK also includes many utilities to perform related tasks such as processing and quality control of high-throughput sequencing data, and bundles the popular Picard toolkit.

These tools were primarily designed to process exomes and whole genomes generated with Illumina sequencing technology, but they can be adapted to handle a variety of other technologies and experimental designs. And although it was originally developed for human genetics, the GATK has since evolved to handle genome data from any organism, with any level of ploidy. 

 

 

GATK consists of many tools each with many parameters. To run GATK effectively, review the GATK best practices documentation:

Software Documentation

Software Documentation Tabs