GATK: Unzipped files Cannot Find GenomeAnalysisTK.jar?

Question

[oars]

I stated with the wget function:

wget https://github.com/broadinstitute/gatk/releases/download/4.0.2.1/gatk-4.0.2.1.zip

I think my problem deals with the gatk-4.0.2.1.zip file. After I unzip the file I can view the contents; however, no where do I see the GenomeAnalysisTK.jar file? I only see the two gatk-package jar files - listed below.

gatk-package-4.0.2.1-spark.jar and gatk-package-4.0.2.1-local.jar

I'm expecting to find the GenomeAnalysisTK.jar file.

Perhaps my instructions are a bit old?

Answer 1

[h.mon]

Now there is a wrapper script called gatk, so you just have to call it. Try gatk with no parameters, or:

gatk --list           Print the list of available tools
gatk Tool --help      Print help on a particular tool

The wrapper is a Python script:

#!/usr/bin/env python
#
# Launcher script for GATK tools. Delegates to java -jar, spark-submit, or gcloud as appropriate,
# and sets many important Spark and htsjdk properties before launch.

[oars]

Thank you, this worked. I also made a shell script that also seemed to do the trick, it was simply:

#!/bin/bash
java -jar /media/dcpattie/backup/Week08/gatk/gatk-4.0.2.1/gatk-package-4.0.2.1-local.jar $*
java -jar /media/dcpattie/backup/Week08/gatk/gatk-4.0.2.1/gatk-package-4.0.2.1-spark.jar $*

[vdauwera]

Please use the gatk wrapper script rather than calling the jars directly. See the docs for an explanation of why. Follow the quick start guide here: https://software.broadinstitute.org/gatk/documentation/quickstart

[anamaria]

Hi,

I am facing the same problem like you. How did you create GenomeAnalysisTK.jar script? I have gatk-4.1.8.1 and also only spark and local jar files...I tried to run ./gatk but I only got options on how to run gatk and GenomeAnalysisTK.jar was not created. Please help.