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

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17 comments

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    ikeoluwao_o

    What happens to unanswered questions in the old forum? Will they somehow still be answered or do we ask them again in the new forum?

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    Geraldine Van der Auwera

    You will need to ask your question again in the new forum. Sorry about that -- I forgot to include that point in my post. If you let them know that it's a repost from the old forum (eg add "Repost: …" in the title), I believe the team will prioritize answering your question. 

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    ikeoluwao_o

    Great! Thank you

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    ajwils

    It would be really good if you guys could find a way to port over the old announcement threads that talked about new features.

     

    For example, the discussion going on in this thread:

    https://gatkforums.broadinstitute.org/gatk/discussion/23598/new-mitochondrial-analysis-with-mutect2#latest

    was useful in my recent work. 

     

    I imagine there were a lot of ongoing discussions that got cut off. Perhaps it might be worthwhile to find a way to fully mirror all the threads that had new posts going back 50-100 days. Maybe mark all the comments as anonymous users?

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    David Murphy

    Have all the old tutorials and documentation been wiped out?

    User experience so far:

    Google "GATK4 haplotypecaller"

    First link: appears to be haplotypecaller Doc... redirects to front page.

    There's countless links from the web and the site itself to pages that now seem to all redirect to the front page.

    For example if I'm trying to follow a guide like this:

    https://github.com/broadinstitute/gatk-docs/blob/master/blog-2012-to-2019/2016-08-17-9_Takeaways_to_help_you_get_started_with_GRCh38.md?id=8180

    It links to "Tutorial#8017" but that link, and indeed most google search results for the entire site (including gatk4) now appear entirely broken.

    There seems to be archived forum posts ... but they link  internally heavily. So someone will ask a question that matches my own problem perfectly and someone will have answered with a link along the lines of "see here[link]"

    But now all links get redirected to the front page.

    This changeover seems to have utterly broken vast quantities of documentation and support.

    I started earlier today thinking I had a simple problem to solve and that there was useful guides to help me but now I'm finding most of the resources unusable.

    this seems to be a bit of a disaster for anyone looking for support.

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    Geraldine Van der Auwera

    Hi David, thanks for reporting this — what you describe is definitely not intentional. It looks like one of the problems you encountered is caused by an inadequate redirect instruction on links that have “guide” in them, which was replaced last year by “documentation”. We’ll fix that ASAP but in the meantime you can find what you need by copying the link and replacing guide by documentation. If you encounter other broken links that don’t fit that pattern, please post them here. I’m sorry it’s been so rocky for you so far.

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    Geraldine Van der Auwera

    Ajwils, to clarify, are you saying it’s the discussion threads specifically that you’d like us to preserve for the new feature announcements? For things like that I think we’d like to try to summarize the information into feature docs rather than keep it around in discussion format. Would that work for you?

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    ajwils

    Geraldine Van der Auwera

    I suppose I am saying that:

    A) The announcement threads themselves should be migrated over as is, as they are a great informational resource for the newer features. This shouldn't be too hard. It's just copy pasting the archived announcements into new announcement threads and fixing any links.

    and 

    B) Find some way to migrate/mirror the actual ongoing discussions, both in those announcement posts, and across the Ask GATK threads. I don' think it would need to go too far back. If this really isn't possible even just for threads with recent posts within the last month or two (I know you are short staffed), then summarized info in feature docs would be good. But honestly, really going through and summarizing two or three months worth of open discussions is probably more work than say making a few hundred threads, copying the code for the original post, then at the bottom of the post (or in a comment) add an archived version of the old page as a saved html attachment.

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    Geraldine Van der Auwera

    Ah I see what you mean, thanks for clarifying. To be frank, we considered doing that but decided to take a different approach in order to boost the sustainability of our knowledge base. Part of why we're in this pickle now is because for far too long, we relied on letting useful information live in announcements and in discussion threads that really should have become part of the main documentation. As a result, we evolved this labyrinthine structure where the information is scattered all over the place, which makes it difficult for people to find in the first place and even harder for us to maintain adequately over time. It's also what makes a migration like this so difficult for everyone. In contrast, if we had a more neatly organized knowledge base with a process to pull in every tidbit of useful information as it materializes in discussion into the main corpus, we'd be in a much better state. That's what we're trying to build with this reboot. So you're right that it would be only a small amount of effort to copy paste content over, but then we'd be perpetuating this semi-chaotic state. We would rather invest a larger amount of effort into laying a better foundation for the future, even if it comes at the cost of some bumpiness during the transition period. 

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    Geraldine Van der Auwera

    David Murphy: I just fixed the issue with the redirects on URLs containing "guide" that you reported. Let me know if you come across any other broken links.

    Thank you for reporting this, it's likely that many others had the same problem but didn't report it. You just did a big favor to a lot of people. 

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    ajwils

    Geraldine Van der Auwera

    I fully respect the choice to trim down, despite being apprehensive about potential lost content. If you're all really prepared to painstakingly port over vast amounts of info into feature docs, well then I wish you luck.

     

    Unrelated side-note, would it be possible to implement the rich format editor for comments and posts, or is this still unavailable for end-users of zendesk? 7 options is pretty barebones.

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    Geraldine Van der Auwera

    Thanks ajwils, we'll do our best not to let you all down. 

    I asked about the editor, unfortunately that's a limitation of Zendesk. Apparently there's an upgrade coming so we'll see what that provides. Is there anything specific you want to be able to do? 

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    ajwils

    Geraldine Van der Auwera

    Off the top of my head:

    • attachments, although in the meantime we can certainly just hyperlink to a filehoster
    • block quotes
    • indentation control
    • code blocks
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    David Murphy

    Thanks so much for the remarkably fast fix!

    I'll let you know if I hit any more but so far what I've tried has worked perfectly!

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    Jacob “Buzz” Roberts

    Can I access GATK release v3.6?

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    David Murphy

    I tried to post another reply here about some other dead links but it just never turned up.

    I'm getting a lot of google links to the site that lead to SSL_ERROR_BAD_CERT_DOMAIN

    https://gatkforums.broadinstitute.org/gatk/discussion/6447/gzipped-gvcf-files

    There also appears to be pages missing from the linked github archive of the forums.

    Is there any up to date zip of the old/removed/moved forum answers?

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    Geraldine Van der Auwera

    Hi David Murphy, sorry I missed your reply. I believe the team is collecting reports etc in the "Other" section of the forum here: https://gatk.broadinstitute.org/hc/en-us/community/topics/360001488892

    The bad cert problem popped up just before the weekend, the team is working on getting that addressed. Sorry about that! 

    Re: missing pages in the github archive, can you give an example? I can try to hunt down whatever's missing and see if there's a bulk fix we can do.

     

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