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Getting an error running Mutect2 wdl (FilterAlignmentArtifacts missing "reference")

Hi,

I'm trying to run the Somatic SNVs and INDELs (mutect2.wdl - GATK 4.1.4.0; https://github.com/gatk-workflows/gatk4-somatic-snvs-indels/blob/master/mutect2.wdl) and I kept getting an error when the workflow gets to the FilterAlignmentArtifacts step. The task reports missing a "reference" argument (-R). I've been able to fix this issue by modifying the wdl to include the reference in the command line of the FilterAlignmentArtifacts.

Was I using the wrong wdl, or using the wdl wrongly?

Thanks,
Pavle

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