Tagged with #forum
2 documentation articles | 3 announcements | 2 forum discussions

Created 2012-11-28 16:47:50 | Updated 2014-06-26 14:32:56 | Tags: forum bug

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Note: only do this if you have been explicitly asked to do so.


You posted a question about a problem you had with GATK tools, we answered that we think it's a bug, and we asked you to submit a detailed bug report.

Here's what you need to provide:

  • The exact command line that you used when you had the problem (in a text file)
  • The full log output (program output in the console) from the start of the run to the end or error message (in a text file)
  • A snippet of the BAM file if applicable and the index (.bai) file associated with it
  • If a non-standard reference (i.e. not available in our resource bundle) was used, we need the .fasta, .fai, and .dict files for the reference
  • Any other relevant files such as recalibration plots

A snippet file is a slice of the original BAM file which contains the problematic region and is sufficient to reproduce the error. We need it in order to reproduce the problem on our end, which is the first necessary step to finding and fixing the bug. We ask you to provide this as a snippet rather than the full file so that you don't have to upload (and we don't have to process) huge giga-scale files.

Here's how you create a snippet file:

  • Look at the error message and see if it cites a specific position where the error occurred
  • If not, identify what region caused the problem by running with -L argument and progressively narrowing down the interval
  • Once you have the region, use PrintReads with -L to write the problematic region (with 500 bp padding on either side) to a new file -- this is your snippet file.
  • Test your command line on this snippet file to make sure you can still reproduce the error on it.

And finally, here's how you send us the files:

  • Put all those files into a .zip or .tar.gz archive
  • Upload them onto our FTP server as explained here (make sure you use the proper UPLOAD credentials)
  • Post in the original discussion thread that you have done this
  • Be sure to tell us the name of your archive file!

We will get back to you --hopefully with a bug fix!-- as soon as we can.

Created 2012-07-20 14:22:00 | Updated 2014-01-24 16:00:04 | Tags: forum developer

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By default, the forum does not send notification messages about new comments or discussions. If you want to turn on notifications or customize the type of notifications you want to receive (email, popup message etc), you need to do the following:

  • Go to your profile page by clicking on your user name (in blue box, top left corner);
  • Click on "Edit Profile" (button with silhouette of person, top right corner);
  • In the menu on the left, click on "Notification Preferences";
  • Select the categories that you want to follow and the type of notification you want to receive.
  • Be sure to click on Save Preferences.

To specifically get new GATK announcements, scroll down to "Category Notifications" and tick off the "Announcements" category for email notification for discussions (and comments if you really want to know everything).

Created 2016-04-13 15:39:47 | Updated | Tags: forum service

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The company that hosts our forums will be performing some maintenance and upgrades on the servers tomorrow, Thursday May 14th. Based on the notification they sent us (included below), we should expect the forums to be unavailable for about ~45 minutes at some point between 2pm and 8pm EST.

During that time, most of the cached GATK documentation will remain available through the Guide section of the GATK website. However, some pages may show error messages and some blog content may not be available, and of course during that time it will not be possible to ask or answer questions on the forum.

Thanks for your patience, and let's all look forward to improved reliability of our forum service.

Notification from our host regarding the planned maintenance:

Maintenance Plan

Starting at 2PM Eastern Time on May 14th, Vanilla's hosting environment will be in a maintenance window for 6 hours. During this time, all nodes in the environment will be rebooted at least once and there will be some instance downtime, which will impact customer forums. We expect the actual down time to last for approximately 45 minutes.


Vanilla is running a virtualized environment on top of the Openstack cloud operating system. Every 6 months a new version of this operating system is released. Vanilla assesses these releases and determines whether or not to upgrade based on the merits of the new features vs. the cost of performing a maintenance with downtime. We have delayed upgrading for the last 2 releases but believe that the version currently available is worth adopting.

During this maintenance period we will also be applying firmware updates to a portion of our compute nodes in order to avoid recently discovered vulnerabilities in their RAID controllers which could cause an outage in the future. This seems like an opportune moment to preemptively get those in.

We expect this OS upgrade to solve some long standing pain points for us and improve our ability to provide consistently high uptime for our customers, so we are excited to move ahead.

Thank you for your understanding!

Created 2013-06-27 03:32:22 | Updated | Tags: Spam forum

Comments (2)

Hello GATK users,

You may have noticed that we have had a spate of spam postings on the forum in the past two days. We apologize for any inconvenience this may have caused you, and would like to assure you that we are working to improve our spam blocking defenses in order to minimize the possibility of further incidents.

We have taken a few immediate measures that may affect your use of the forum.

First, all new users will now be required to confirm their email before they are allowed to post any comments. If you find yourself suddenly unable to post, it may be that your status is still "unconfirmed". If so, please retrieve the email you originally received from the forum system when you registered, and click the confirmation link it contains. If you cannot find that email, you can have the system issue resend one to you.

Second, we have increased the "freeze period" between postings. You will now have to wait two minutes between postings (whether you are posting new discussions or commenting on existing ones). The reason for this is that most spammers want to make several postings in a very short time. If they are made to wait, they give up. This should limit the likelihood that we'll see more spates of a dozen messages at a time, which is what we saw tonight and is particularly obnoxious. Based on the normal forum usage we have seen this should not be a problem for real users. However if you find that this is too stringent, please let us know in this thread.

Thank you for your patience and understanding. As always, we welcome your feedback and suggestions.

Created 2013-01-07 19:02:39 | Updated 2013-01-07 21:02:54 | Tags: forum community

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We've realized that having separate Team / Community Q&A sections is confusing and unnecessary, so we are going to merge the two. From now on there will only be one Q&A section (Ask the Team). We invite you to ask any questions related to the GATK and its application in that category. We welcome answers and comments from everyone in the community in these discussions; if you know something, say something! And of course you are also always welcome to comment on tool and method documentation articles.

Created 2014-10-14 17:48:28 | Updated | Tags: forum

Comments (4)

I was wondering if perhaps there should be a sub-forum or some other such area dedicated to work on non-model organism?

Those of us working on non-model organisms (or even just non-human/mouse) face quite a few issues which folks working on humans don't. There are also a lot of (sophisticated) workflows, optimizations, and even terms which are used with human data which just don't apply to other organisms (except maybe mouse models).
It really boils down to: "Do you have a very good reference sequence and lots of annotations, or not".

Some of the topics would include:

  • Pretty much everything when your population has a lot of variation (relative to humans at least)
  • Variant calling with different ploidy (thankfully HC can now do)
  • Reference-free methods
  • What I'll call 'reference-lite' methods, where the reference is a guide but not really trusted
  • Detecting and dealing with reference errors (gaps, chimeras, misassembly, ect.)
  • Detecting big structural variants (eventually GenomeSTRiP should help)

Anyways, just an idea. I'm curious if there is enough interest in expanding the GATK toolset and best-practices to be more useful for non-model organisms.

Created 2013-12-18 19:03:19 | Updated 2013-12-18 19:03:55 | Tags: forum

Comments (1)

When you copy from a code block on the forum, it adds a message to the text you copy saying "See more at http://gatkforums.broadinstitute.org/". Could it not do this?