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RealignerTargetCreater: A USER ERROR has occurred: '-T' is not a valid command.

I was running GATK RealignerTargetCreater . I ran the same command before with another bam file and it ran fine. Both of the bam files were produced using BWA MEM, sorted, indexed, fixed mate information (samtools) and then duplicate removed by PICARD.

My command is as follows:
java -jar GenomeAnalysisTK.jar \
-T RealignerTargetCreator \
-R reference.fasta \
-I input.bam \
--known indels.vcf \
-o forIndelRealigner.intervals

In the end, the error were occured:

A USER ERROR has occurred: '-T' is not a valid command.

Set the system property GATK_STACKTRACE_ON_USER_EXCEPTION (--java-options '-DGATK_STACKTRACE_ON_USER_EXCEPTION=true') to print the stack trace.

It would be most helpful if someone can tell me how to solve this problem. Many thanks in advance.


  • SheilaSheila Broad InstituteMember, Broadie, Moderator


    Have you resolved this? It looks like your command may have some extra space between GenomeAnalysisTK.jar and -T RealignerTargetCreator. Are you using the \ ? Perhaps try removing those.


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