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

(How to) Execute Workflows from the gatk-workflows Git Organization Follow

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    Naomi Dyer

    I tried following the instructions to run locally but seem to run into problems - I get error messages when executing the workflow . I think it is because I failed to edit the json file correctly. If I just replace the path to the bam file and then attempt to exectue, the error message says 

    [2021-09-22 13:49:26,73] [error] WorkflowManagerActor Workflow 82ae9bf6-b62a-43b6-87ca-c874e73a0715 failed (during MaterializingWorkflowDescriptorState): cromwell.engine.workflow.lifecycle.materialization.MaterializeWorkflowDescriptorActor$$anon$1: Workflow input processing failed:
    Unexpected character '#' at input index 4 (line 2, position 3), expected '"':
    ##Comment1:Input,

    I also tried removing all the comment lines, but then I get an error that says that V is an unexpected character. I imagine it is because I have absolutely no idea what I'm doing with .json file editing, but just wanted to check if these error messages would be expected? Where in the .json file does the valid docker container have to go?

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