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problem locating program
I downloaded GenomeAnalyserTK-2.3-9-ge53bf34 onto my computer and it works with java. The problem is that it can't find the walker with the name RealignerTargetCreator when I use the command.
bash-3.2$ java -jar /usr/bin/GenomeAnalysisTK.jar -T RealalignerTargetCreator -R reference.fasta -o output.interval -I test_sorted.bam
ERROR MESSAGE: Invalid command line: Malformed walker argument: Could not find walker with name: RealalignerTargetCreator
I noticed that the resource file only contained CountLoci.java, CountReads.java, Depth of Coverage.java,Pileup.java,PrintReads.java and ValidatingPileup.java.
Could someone help me with this problem?