Hi all,

We are organizing a two-day GATK workshop to be held at the Broad Institute in Cambridge, MA on Dec 4-5 2012.

This workshop will focus on the core steps involved in calling variants with the Broad’s Genome Analysis Toolkit, using the “Best Practices” developed by the GATK team. You will learn why each step is essential to the calling process, what are the key operations performed on the data at each step, and how to use the GATK tools to get the most accurate and reliable results out of your dataset.

The workshop will last two days, divided into lecture-style sessions in the morning and optional hands-on sessions in the afternoon (note that for practical reasons, attendance at the latter will be limited, so be sure to sign up early). In the morning, you’ll hear from the GATK development team, who will explain the rationale, theory and real-life applications of the Best Practices. In the afternoon, the GATK team will help you work through interactive exercises and tutorials in which you will apply the Best Practices to real datasets.

Registration is not yet open; we will post another announcement when it is, but be sure to save the date if you are interested in attending.

Please note that this workshop is primarily intended for Cambridge and Boston-area users; users from further afield are welcome to come, but at this time we regretfully cannot offer any financial assistance for travel or lodging. Rest assured that we will make videos of the talks and all teaching materials available online following the workshop.



pwhite on 10 Oct 2012


Thanks so much for doing this, it will be really helpful. I'd like to send a member of my lab, but will need to make travel arrangements. Do you have an approximate start and end-time for the meeting?

Geraldine_VdAuwera on 10 Oct 2012


Times aren't entirely final yet, but most probably, morning sessions will run from 9 to 12:30, afternoon sessions will be 1:30 to 4 pm.

saumya on 10 Oct 2012


Hi. When will the registration open for this workshop? Thanx

Geraldine_VdAuwera on 10 Oct 2012


We're hoping to open registration on Friday (Nov 16).

cardillox on 10 Oct 2012


I would be great to attend to it. Unfortunately I am in England. I was wondering if the material for the workshop will be available. It would be very useful. Thank you

Geraldine_VdAuwera on 10 Oct 2012


Yes, we'll put the slide decks and video of the talks on the website.

auzun on 10 Oct 2012


Hello, Is the registration link going to be available today? Thanks.

Geraldine_VdAuwera on 10 Oct 2012


Yes, here it is: http://www.regonline.com/builder/site/Default.aspx?EventID=1162708

auzun on 10 Oct 2012


Great Thanks!

chung2000 on 10 Oct 2012


Will there be videos available of the workshops? I was called back into work before I could sit through all the presentations :-(

Geraldine_VdAuwera on 10 Oct 2012


Yes, the talks were recorded and videos will be available in a few weeks. In the meantime, the slides of the presentations are all online -- see the latest announcement on this forum for the link.

chung2000 on 10 Oct 2012


Thank you very much Geraldine. The slides will be very useful to start discussions with colleagues.

AhmedEzat on 10 Oct 2012


Very useful slides thanks for sharing Cheers [Ahmed Ezat](http://controlrank.com)




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