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RealignerTargetCreator of version GenomeAnalysisTK-1.0.5974 doesn't recognize the argument 'known'

jlkuanjlkuan SingaporeMember
edited January 2016 in Ask the GATK team

I ran the following command:
java -Xmx2g -jar GATK/GenomeAnalysisTK-1.0.5974/GenomeAnalysisTK.jar -et NO_ET -T RealignerTargetCreator -R hg19.fa -known Mills_and_1000G_gold_standard.indels.b37.vcf.gz -I hg19.sorted.bam.dedup_reads.bam -o forInderRealigner.intervals

But I got the following error:
Picked up _JAVA_OPTIONS: -XX:+UseSerialGC

ERROR ------------------------------------------------------------------------------------------
ERROR A USER ERROR has occurred (version 1.0.5974):
ERROR The invalid arguments or inputs must be corrected before the GATK can proceed
ERROR See the documentation (rerun with -h) for this tool to view allowable command-line arguments.
ERROR Visit our wiki for extensive documentation
ERROR Visit our forum to view answers to commonly asked questions
ERROR MESSAGE: Argument with name 'known' isn't defined.
ERROR ------------------------------------------------------------------------------------------

Thus, may I know the equivalent argument to 'known' for version 1.0.5974? Thanks.

Best Answer


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