GATK: how to find and use GenomeAnalysisTK.jar under java

Question

[Yingzi Zhang]

I downloaded the gatk-4.0.6.0 package and unzipped it. I need to run the command java -jar GenomeAnalysisTK.jar but I couldn't find where GenomeAnalysisTK.jar is. How please? The list in the package are the followings.

gatk                           gatk-package-4.0.6.0-local.jar  scripts
gatk-completion.sh             gatk-package-4.0.6.0-spark.jar  setup_gcnvkernel.py
gatkcondaenv.intel.yml         gatkPythonPackageArchive.zip    setup.py
gatkcondaenv.yml               gatktool                        setup_vqsr_cnn.py
GATKConfig.EXAMPLE.properties  gcnvkernel                      vqsr_cnn
gatkdoc                        README.md

Answer 1

[GenoMax]

Did you look at the Quick start guide for GATK v.4.x?

Command you are asking about is from older version of GATK v.3.x.

[Yingzi Zhang]

Yes, and I see many slight differences in options description. Thank you!