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.


In addition to the measures outlined above, we have now activated a review process for new user registrations. We realize that this may cause some delays to legitimate users who sign up for the first time, and we regret the inconvenience it may cause. However, since we put this in place less than 24 hours ago, it has already caught and blocked ~30 attempts by spammers to infiltrate our community. Right now it is the most effective defense we have. We will of course keep working to improve our defenses and to reduce delays on legitimate new user registrations. If you are one of those affected, we thank you for your patience and make you a promise: it will be worth it.

Thu 27 Jun 2013


Status update on the spam front: we've installed a new spam-blocking plugin that seems to be catching all the incoming spam now. We're going to leave the registration on "high alert" manual review mode for a few days, and if in that time we don't see anymore spam get through the automatic filter, we'll take the registration back down to automatic mode.

Thu 27 Jun 2013

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GATK Dev Team


@hoffsbeefs Yes, multithreading can explain some marginal differences. For purely deterministic behavior, it should be disabled.
25 Oct 16
@hoffsbeefs Yes it should be deterministic, given same data, same parameters and no multithreading.
25 Oct 16
RT @BroadGenomics: Missed #GATK WKSP at #ASHG16? 10am meet Geraldine at booth 329 - Broad’s GATK Guru @gatk_dev #BroadGenomicsExperts https…
20 Oct 16
RT @NJL_NGS: Broad Institute Workbench workshop now at #ashg16. https://t.co/t6L452mp8a
19 Oct 16
RT @konradjk: We're rebranding a bit! gnomAD now adds WGS regions, as well as doubling the data depth and increasing diversity (5K ASJ!) #A…
19 Oct 16

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Had a really nice time in Vancouver at #ASHG16, also known as "The @dgmacarthur Lab Meeting"
24 Oct 16
Real motivation behind gnomAD: all of you have now learnt the proper capitalization of ExAC, and we felt you needed a new challenge. #ASHG16
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Asked a question, speaker jokes not to edit your BAM header and expect GATK to let you get away with it.
19 Oct 16
My new hobby: finding incomprehensible diagrams on office whiteboards and adding alarming conclusions to them https://t.co/7RAzBF0kYh
30 Sep 16
I've easily written my first custom ReadFilter for GATK. The @gatk_dev 's toolkit is a great example of programming.
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