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

Question

[hafiz.talhamalik]

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.

[Pierre Lindenbaum]

show us the command line.

[hafiz.talhamalik]

[WouterDeCoster]

Just add the command.

[hafiz.talhamalik]

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

[WouterDeCoster]

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.

[hafiz.talhamalik]

ok. let me try with this

Answer 1

[hafiz.talhamalik]

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 ?

[WouterDeCoster]

https://gatkforums.broadinstitute.org/gatk/discussion/11455/realignertargetcreator-and-indelrealigner

Answer 2

[Mohammed]

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