Introduction

Genome Analysis Toolkit (GATK), as the name implies, is a toolkit for analyzing genomes. Its main feature is to find variants and genotypes for variant calling from sequencing data, including SNP and INDEL.

GATK includes the following tools:

• Diagnostics and quality control tools
• Sequence data processing tools
• Variant discovery tools
• Variant evaluation tools
• Variant manipulation tools
• Commenting modules
• Reads filtering
• Resource file decoding tools
• Reference sequence utilities

GATK4 is the latest GATK version released by Broad Institute in January 2018. Compared with the previous version, this version has major changes, including newly developed processes and the latest tools based on machine learning algorithms. GATK4 greatly optimizes the performance, computing speed, interface flexibility, and scalability. The end-to-end process can run locally or on the cloud. In addition, it is developed based on Spark and supports cluster deployment.

For more information, visit the official GATK website.

Programming language: Java

Brief description: A toolkit for analyzing genomes.

Open source license: BSD 3-Clause "New" or "Revised" License