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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

Input configuration for GATK4-gCNV workflow on Terra

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    Samantha (she/her)

    Hi Seunghun Han,

    Thanks for writing in. We'll take a look at your question and get back to you as soon as we can.

    Best,

    Samantha

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    Seunghun Han

    Hi Samantha (she/her),

    Is there any update on this? 

    thanks,
    Seunghun 

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    Samantha (she/her)

    Hi Seunghun Han,

    The contig_ploidy_priors and intervals inputs are something you need to generate (with with WES data you'll need to start with the list of targets provided by the capture kit manufacturer). The instructions on their format and how to generate them can be found in the tutorial article you linked and this article.

    The  mappability_track_bed and segmental_duplication_track_bed files were in a private bucket, but they should now be in gs://gatk-best-practices/cnv-germline-pipeline.

     

    Best,

    Samantha

     

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    Seunghun Han

    Thanks a lot!!! This is exactly what I need. 

    Best,
    Seunghun

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