Realigner Target Creator
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Entering edit mode
5.3 years ago
sukesh1411 ▴ 30

Hi

I am currently using GATK-1.0 version to run the RealignerTargetCreator to perform local realignment around indels.
command: java -jar GenomeAnalysisTK.jar -T RealignerTargetCreator -R ../../rice/IRGSP-1.0_genome.fasta -I uniqueKAVUNI1.bam -known oryza_sativa.vcf -o target_intervals.list. I end up with below error

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 Please do not post this error to the GATK forum
ERROR
ERROR See the documentation (rerun with -h) for this tool to view allowable command-line arguments.
ERROR Visit our wiki for extensive documentation http://www.broadinstitute.org/gsa/wiki
ERROR Visit our forum to view answers to commonly asked questions http://getsatisfaction.com/gsa
ERROR
ERROR MESSAGE: Argument with name 'known' isn't defined.</h5>

I tried --variant and --known option too to submit the known vcf file. I get the same error. I want to know what is the input argument given to submit the vcf file.

Thanks

software error • 2.5k views
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Entering edit mode
5.3 years ago
abedkurdi10 ▴ 70

hi sukesh1411, -L target_intervals.list -o output_file.intervals --known oryza_sativa.vcf

i think this should fix your error.

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Entering edit mode

Hi

Thank you sir. Again the same error if i use the --known. As i said i tried -known, -- known --variants. Will the version of tool matters?

Thanks

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maybe, i am using gatk 3.6 which is the latest version.

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Entering edit mode
5.3 years ago
vakul.mohanty ▴ 250

You can migrate to the latest version of GTAK. Also the present best practices pipeline has done away with the indel realignment step (https://software.broadinstitute.org/gatk/best-practices/bp_3step.php?case=GermShortWGS)

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thank you sir. i will try in latest version of GATK.

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