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GATK Error Message: Invalid argument value 'RealignerTargetCreator at position' 0

I am using gatk 3.7 and trying to make a vcf file from sam file using gatk pipeline. I am getting an error Error Message: Invalid argument value 'RealignerTargetCreator at position' 0 why i am getting this error message.

snp vcf gatk
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updated by Mohammed • Mohammed • written by hafiz.talhamalik hafiz.talhamalik

java -jar GenomeAnalysisTK.jar RealignerTargetCreator -R hg38.fa -o target.list -I makred.bam

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written by hafiz.talhamalik hafiz.talhamalik

The example from the GATK documentation is the following:

 java -jar GenomeAnalysisTK.jar \
   -T RealignerTargetCreator \
   -R reference.fasta \
   -I input.bam \
   --known indels.vcf \
   -o forIndelRealigner.intervals

There is a difference with your command, concerning RealignerTargetCreator.

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written by WouterDeCoster WouterDeCoster

2 answers

One more thing. GATK 4 doesn't have the option of TargetRealignmentCreator, so what's the alternate of it ? do we apply haplotype caller directly on marked-duplicate.bam file ?

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written by hafiz.talhamalik hafiz.talhamalik

add -T RealignerTargetCreator to your command line after the jar file it will solve the problem.

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written by Mohammed • Mohammed

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