Realigner Target Creator

Question

[sukesh1411]

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

Answer 1

[abedkurdi10]

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

i think this should fix your error.

[sukesh1411]

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

[abedkurdi10]

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

Answer 2

[vakul.mohanty]

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)

[sukesh1411]

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