Where is the list of annotations and annotation groups?
Answered
Documentation for several GATK tools such as HaplotypeCaller and Mutect2 include a description of arguments --annotation and --annotation-group, but these descriptions do not say what annotations and annotation groups are available. Search for "annotation groups" or "annotation group list" or "list of annotation groups" or "where can I find a list of annotation groups" turns up a long list of search results that are essentially nothing more than references to pages that describe the same --annotation and --annotation-group arguments.
Surely there MUST be a page listing these things, and surely that page should be easily accessible through site searches and even via general web searches?
-
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
-
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
-
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
-
Thanks.
-
I'll ask here too, what about the content of each annotation group? How can we know the differences between each group?
-
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
-
Agreed that the annotations should have their own page to be more searchable
Please sign in to leave a comment.
7 comments