The GATK has a new website and forum!

[vdauwera]

The new GATK website, released in parallel with GATK version 2.0 (beta) features a much improved documentation system and user-friendly introductory materials for new users. Also, the forum is now integrated into the website and linked to the documentation, making it much easier to refer to the docs in forum discussions and find relevant information.



If you hated the old Wiki, you're going to love this.

http://www.broadinstitute.org/gatk/

[adaptivegenome]

I like it! Can't wait till you guys load the guide...

[vdauwera]

Working on it as we speak

[GRT]

Is the GSA public FTP server up yet?

[vdauwera]

Yes the FTP is up, that hasn't changed. See this thread for instructions:

http://gatk.vanillaforums.com/discussion/1215/how-can-i-access-the-gsa-public-ftp-server

If you have any trouble accessing it, let us know in the GATK forum.

[adaptivegenome]

The guide looks great. This is a really nice website!

[vdauwera]

Thanks, glad you like it! We're still working on migrating the knowledge base from the old wiki and refining the search/content linking features, so be sure to check back often.

Of course we welcome all feedback, suggestions and constructive criticism; the website is for all of you, so it helps if you tell us how we can make it better.

[honey]

I have always liked changes and improvement, However You are messing up something in GATK web page, The page of instructions for best practice is no where matching to your download version. I spend several hrs and discussed with my more educated colleagues and this mess is there. Sorry

[vdauwera]

Hi there,

I apologize if you've had trouble finding the Best Practices page. These past few days we were installing new features which caused some intermittent breakdowns in service for the Guide pages. These are growing pains that will not persist once we are out of beta status.

The latest version of the Best Practices are now restored at
http://www.broadinstitute.org/gatk/guide/best-practices

If you ever have such troubles again please post a message in the GATK forum. During EST business hours we usually respond almost immediately if it is a simple question or problem, and we can save you hours of frustration.

Thank you for your patience while we sort out these initial difficulties, and please check back often!

[honey]

Gatk

I guess I will post one more question here- What I am trying to say is
http://www.broadinstitute.org/gatk/guide/best-practices

explain GATK version 4 release 2.0, However when I download GATK from

http://www.broadinstitute.org/gatk/download
The release is 2.0 but version is different so I believe instructions are different.
I download Download GATK2.0 not Download queue

Am I missing something??

Thanks for your quick response.

[vdauwera]

Oh, that's an interesting misunderstanding, I'm glad you asked because we need to make that clearer. What you are seeing is version 4 of the Best Practices document, which applies to GATK 2.0 (any release number).

Does that help? We will try to name things more clearly in order to avoid this confusion in future.