GATK: GenomeAnalysisTK.jar file

[jorge]

Hello all,

I’m 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?

I’d be grateful if someone could please clarify on this.

Thanks
Jorge

[orionzhou]

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:

http://www.broadinstitute.org/gsa/wiki/index.php/Downloading_the_GATK

[ulz_peter]

.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.