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

Tracks for germlineCNV calling AnnotateIntervals

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    Genevieve Brandt (she/her)

    Hi Zsofia Ratkai,

    Please see this featured workspace for the segmental duplication track file and mappability track file. We generally also have 150 base pair read length reads, so you are fine to use whatever resources are in the featured workspace.

    If the resources you want are not in the featured workspace, we can ask one of our collaborators to post them. Please let me know.

    Best,

    Genevieve

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    Pamela Bretscher

    Hi Zsofia Ratkai,
    I am going to move your post into our Community Discussions -> General Discussion topic, as the germline topic is for reporting bugs and issues with GATK.
    You can read more about our forum guidelines and the topics here: Forum Guidelines.


    Best,
    Pamela

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    Genevieve Brandt (she/her)

    Hi Zsofia Ratkai,

    For your second question, could you provide your command and complete log? Did you merge overlapping intervals? If so, how did you do it?

    Thank you,

    Genevieve

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