GATK HaplotypeCaller Error

Question

[julianneradford]

Hi there! Hi there,

I am trying to run GATK's (v 4.1.9.0) 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 \
 - ERC GVCF

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. Thanks!

Answer 1

[Pierre Lindenbaum]

remove the spaces bewteen the - and the name of the optionsO

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