Question: GATK: Unzipped files Cannot Find GenomeAnalysisTK.jar?
gravatar for oars
3.0 years ago by
oars160 wrote:

I stated with the wget function:


I think my problem deals with the 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- and gatk-package-

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

Perhaps my instructions are a bit old?

gatk • 5.0k views
ADD COMMENTlink modified 3.0 years ago by h.mon32k • written 3.0 years ago by oars160
gravatar for h.mon
3.0 years ago by
h.mon32k wrote:

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.
ADD COMMENTlink written 3.0 years ago by h.mon32k

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

java -jar /media/dcpattie/backup/Week08/gatk/gatk- $*
java -jar /media/dcpattie/backup/Week08/gatk/gatk- $*
ADD REPLYlink written 3.0 years ago by oars160

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:

ADD REPLYlink written 3.0 years ago by vdauwera990


I am facing the same problem like you. How did you create GenomeAnalysisTK.jar script? I have gatk- 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.

ADD REPLYlink written 5 months ago by anamaria140
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 2654 users visited in the last hour