GATK: how to find and use GenomeAnalysisTK.jar under java
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Entering edit mode
2.7 years ago
Yingzi Zhang ▴ 60

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
software error • 2.5k views
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Entering edit mode
2.7 years ago
GenoMax 99k

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.

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

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