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This article mainly introduces what GATK4 is, has a certain reference value, interested friends can refer to, I hope you can learn a lot after reading this article, the following let the editor take you to understand it.

GATK, the abbreviation of Genome Analysis ToolKit, is a software to analyze variation information from high-throughput sequencing data. It is one of the most mainstream snp calling software at present. GATK was originally designed to analyze human full exon and whole genome data. With the development, it can also be used in other species. It also supports the detection of CNV and SV mutation information. On the official website, a complete analysis process is provided, called GATK Best Practices.

The latest version of this article is 4.1.2.0, called GATK4. Compared with the previous version, GATK4 optimizes the algorithm, improves the running speed, and integrates the functions of picard software. GATK4 is based on the java language and requires java version 1.8. Download links are as follows

Https://software.broadinstitute.org/gatk/download/

The installation process is as follows:

Wget https://github.com/broadinstitute/gatk/releases/download/4.1.2.0/gatk-4.1.2.0.zip

Unzip gatk-4.1.2.0.zip

Tree-L 1 gatk-4.1.2.0/

Gatk-4.1.2.0/

├── gatk

├── gatk-completion.sh

├── gatkcondaenv.yml

├── GATKConfig.EXAMPLE.properties

├── gatkdoc

├── gatk-package-4.1.2.0-local.jar

├── gatk-package-4.1.2.0-spark.jar

├── gatkPythonPackageArchive.zip

└── README.md

After unzipping, you can see two files with the suffix .jar, local for running locally and spark for running on the spark cluster. In actual use, just use the executable file gatk directly.

Use a simple command to see if the program is installed correctly

Gatk-list

This command can print out all the subcommands, and if the result is printed, the program is installed correctly. A screenshot of the partial command is as follows

If there is (picard) after the subcommand, it means that this function is inherited from the picard software. From here, we can also see that GATK4 integrates the functions of the picard software. There is no need to mix picard and gatk as in previous versions.

Thank you for reading this article carefully. I hope the article "what is GATK4" shared by the editor will be helpful to you. At the same time, I also hope you will support us and pay attention to the industry information channel. More related knowledge is waiting for you to learn!

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