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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

Where is the list of annotations and annotation groups?

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    Pamela Bretscher

    Hi tedtoal,

    At the bottom of the tool index for GATK, there is a section labeled "Variant Annotations" that contains a list of available annotations for various GATK tools. 

    Please let me know if this does not answer your question or wasn't what you were looking for.

    Kind regards,

    Pamela

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    tedtoal

    Thanks.  I STRONGLY suggest that you separate this list into its own web page and make sure its title says something like "Annotation List for Variants", something that your search engine will find as about the FIRST hit if someone searches for "Annotations".

    Ted

     

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    Pamela Bretscher

    Hi tedtoal,

    Thank you for this suggestion. The GATK team will look into making the list more accessible. I'm glad you were able to find what you were looking for. 

    Kind regards,

    Pamela

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    Pamela Bretscher

    Hi Patrick Jongeneel,

    Here is a link to an old forum post where a user created a text document summarizing the annotations included in each annotation group. I don't believe this information has been added to the GATK documentation yet but the GATK team is working on updating the annotation documentation. https://sites.google.com/a/broadinstitute.org/legacy-gatk-forum-discussions/2019-02-11-2018-08-12/12809-How-do-we-view-the-specific-annotations-in-each-annotation-group

    Kind regards,

    Pamela

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    tedtoal

    Thanks.

     

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    Patrick Jongeneel

    I'll ask here too, what about the content of each annotation group? How can we know the differences between each group? 

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    Layne Sadler

    Agreed that the annotations should have their own page to be more searchable

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