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GATK 4 VariantRecalibrator example using unavailable option: --recal-file

cr517cr517 CambridgeMember

Hi,

On this page: https://software.broadinstitute.org/gatk/documentation/tooldocs/current/org_broadinstitute_hellbender_tools_walkers_vqsr_VariantRecalibrator.php

VariantRecalibrator is using --recal-file it the example command. However, this option is not available to the tool. Do you mean --output, which is described in the help of the tool as The output recal file used by ApplyRecalibration Required.?

Answers

  • SheilaSheila Broad InstituteMember, Broadie, Moderator admin

    @cr517
    Hi,

    VariantRecalibrator is using --recal-file it the example command. However, this option is not available to the tool.

    What do you mean? Do you get an error message?

    -Sheila

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