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Old 06-05-2011, 03:22 AM   #1
Location: Madrid, Spain

Join Date: Jun 2011
Posts: 25
Default GATK: GenomeAnalysisTK.jar file

Hello all,

Im nuclear about what should contain the GenomeAnalysisTK.jar file.

This is how the command line looks like:
java -jar GenomeAnalysisTK.jar -R exampleFASTA.fasta -I exampleBAM.bam -T CountLoci -o output.txt

My questions are:
1. what is the GenomeAnalysisTK.jar file? Does it just contain .dict and the .fai files?
2. can the GenomeAnalysisTK.jar be just substituted by the path where the corresponding files (whatever they are) are located? Otherwise is there a specific way to compress that folder and created the jar file?

Id be grateful if someone could please clarify on this.

jorge is offline   Reply With Quote
Old 06-05-2011, 08:36 PM   #2
Location: St. Paul

Join Date: Sep 2009
Posts: 14

Hi, you need to download the toolkit and type in the path in the command, e.g.:
java -jar /path/to/GenomeAnalysisTK.jar [options]
The toolkit can be downloaded from:
orionzhou is offline   Reply With Quote
Old 06-05-2011, 08:59 PM   #3
Senior Member
Location: Graz, Austria

Join Date: Feb 2010
Posts: 219

.jar files are compressed java source code files (Java ARchive). This file is actually the program. It does not contain the .dict and the .fai files.
I didn't understand your second question, but as stated before there is no genome-specific file in the source-code archive.
ulz_peter is offline   Reply With Quote

dict, fai, gatk, jar

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