Genome Analysis Toolkit

Variant Discovery in High-Throughput Sequencing Data

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Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size. Learn more

GATK4.2.3.0 HaplotypeCaller error


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    Pamela Bretscher

    Hi Alicia,

    It looks like this error is coming from a typo in the command that you ran. The tool is providing this error: A USER ERROR has occurred: Illegal argument value: Positional arguments were provided ', }' but no positional argument is defined for this tool. This indicates that the tool isn't reading your command properly. Could you check to ensure that there are no additional or missing spaces in your command, etc.? Here is a similar post with the same issue.

    Kind regards,


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