Question: Realigner Target Creator
0
gravatar for sukesh1411
7 months ago by
sukesh141130
South Africa
sukesh141130 wrote:

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 • 281 views
ADD COMMENTlink modified 4 days ago by Biostar ♦♦ 10 • written 7 months ago by sukesh141130
1
gravatar for abedkurdi10
7 months ago by
abedkurdi1020
abedkurdi1020 wrote:

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

i think this should fix your error.

ADD COMMENTlink written 7 months ago by abedkurdi1020

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

ADD REPLYlink written 7 months ago by sukesh141130

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

ADD REPLYlink written 7 months ago by abedkurdi1020
0
gravatar for vakul.mohanty
7 months ago by
vakul.mohanty220
United States
vakul.mohanty220 wrote:

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)

ADD COMMENTlink written 7 months ago by vakul.mohanty220

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

ADD REPLYlink written 7 months ago by sukesh141130
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