gravatar for julianneradford

2 hours ago by

Hi there!
Hi there,

I am trying to run GATK's (v HaplotypeCaller using CLI on my Mac to acquire VCFs from some bam files, using this command for the first file:

 ./gatk HaplotypeCaller 
 - R Rflav_transcriptome_sequences.fa 
 - I SRR5341585.bam 
 - O 85variants.g.vcf 

but on the first bam file I tried to do, I am received this error:

A USER ERROR has occurred: Illegal argument value: Positional arguments were provided ',-{R{Rflav_transcriptome_sequences.fa{-{I{SRR5341585.bam{-{O{85variants.g.vcf{-{ERC{GVCF}' but no positional argument is defined for this tool.

Does anyone know how to fix the "no positional argument is defined for this tool" error? I am not sure what this means and cannot find any online help.

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