A USER ERROR has occurred: no positional argument is defined for this tool.
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10 months ago

Hello, hope all are doing well.

I am running the HaplotypeCaller command to generate the variant file by giving multiple input bam files in a single command.

python3 gatk --java-options -Xmx7g HaplotypeCaller --reference ref.fasta --input file1.bam file2.bam --sample-ploidy 12 --standard-min-confidence-threshold-for-calling 30 --tmp-dir /path/gatk-4.1.8.1 --output comb.vcf


But i am getting the following error

A USER ERROR has occurred: Illegal argument value: Positional arguments were provided ',file1.bam}' but no positional argument is defined for this tool.


I think there is something wrong in the command line most probably in the input argument or in sample ploidy. May be this is not the correct way to give multiple bam files. Kindly guide where is the problem in command line or how to state multiple bam files in a single command line.

GATK4 HaplotypeCaller BAM • 317 views