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Can I use GATK workflow for plant (Cannabis) to detect variants?

NandaNanda CanadaMember

Can I use GATK workflow for plant (Cannabis) to detect variants?

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  • SheilaSheila Broad Institute admin
    Accepted Answer

    @Nanda
    Hi,

    Yes to both of your questions. @SkyWarrior is correct that knowing the ploidy of your plant is important (so you can set it in the variant caller). Other than that, you should be able to use the Best Practices.

    For RNA-seq data, we are working on the Best Practice, so they are not fully available yet.

    -Sheila

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