I have reference genome as hg19.fa and duplicate removed reads using picard as deduped_reads.bam. Next, I am trying to run the command
java -jar /home/snijeshv/bin/GenomeAnalysisTK-3.7/GenomeAnalysisTK.jar -T RealignerTargetCreator -R hg19.fa -I deduped_reads.bam -o realignment_targets.list
but I am getting an error as follows:
~/Desktop/Genome$ java -jar /home/snijeshv/bin/GenomeAnalysisTK-3.7/GenomeAnalysisTK.jar -T RealignerTargetCreator -R hg19.fa -I deduped_reads.bam -o realignment_targets.list
##### ERROR ------------------------------------------------------------------------------------------
##### ERROR A USER ERROR has occurred (version 3.7-0-gcfedb67):
##### ERROR
##### ERROR This means that one or more arguments or inputs in your command are incorrect.
##### ERROR The error message below tells you what is the problem.
##### ERROR
##### ERROR If the problem is an invalid argument, please check the online documentation guide
##### ERROR (or rerun your command with --help) to view allowable command-line arguments for this tool.
##### ERROR
##### ERROR Visit our website and forum for extensive documentation and answers to
##### ERROR commonly asked questions https://software.broadinstitute.org/gatk
##### ERROR
##### ERROR Please do NOT post this error to the GATK forum unless you have really tried to fix it yourself.
##### ERROR
##### ERROR MESSAGE: Invalid command line: Malformed walker argument: Could not find walker with name: RealignerTargetCreator
##### ERROR
i have figured out....
It is compatibility issue of bwa with picard tools
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