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Wed, 10/22/2014 - 14:56

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Call about writing GIAB papers scheduled for Friday, October 3

We have scheduled a call about strategy for writing papers at 2pm EDT on Friday October 3. The call-in number will be (559) 726-1300; Passcode 135879#. To start the discussion, I've created short outlines of several papers that I've either discussed with others or started to write. We will discuss whether and how to combine these and other ideas, and how to prioritize them:
https://drive.google.com/file/d/0B7Ao1qqJJDHQUmJUa0lTd0RCM3M/edit?usp=sh...

Cheers,
Justin

First data from GIAB PGP Trios on FTP

The first data from the Personal Genome Project (PGP) trios that we plan to make into NIST Reference Materials is now on the GIAB ftp site. Complete Genomics has sequenced both the Ashkenazim and Asian trios from the PGP and uploaded the data to:
ftp://ftp-trace.ncbi.nih.gov/giab/ftp/technical/complete_data/trios

Workshop Summary and Slides from August 2014

Thank you to all of you participated in our GIAB workshop August 14-15. It was great to have discussions with many of you. Below is a summary of talks and discussions from the workshop. Most of the slides are available on slideshare at http://www.slideshare.net/GenomeInABottle, and some additional slides may be posted in the next couple weeks. We plan to hold the next GIAB Consortium workshop Jan 29-30, 2015 at Stanford University, and we hope to see many of you there then!

Travel and Webinar information for workshop tomorrow and Friday

We are looking forward to seeing many of you for the Genome in a Bottle Workshop at NIST tomorrow and Friday. For those of you who registered online, you should receive "dash passes" by email that you can print to allow you to enter campus quickly without going into the visitor center. The workshop will begin in the Green Auditorium in the Administration Building (101).

Agenda for August 2014 GIAB Workshop

We are looking forward to seeing many of you at the GIAB workshop in two weeks, August 14-15, 2014. We have now posted a draft of the agenda for the workshop at https://docs.google.com/spreadsheets/d/1S1h2FVnQKGf-Egyfx6IaUnrWLil1YXoW....

Are you using our high-confidence calls?

For our upcoming GIAB workshop, we'd like to collect some examples of how people are using our high-confidence calls for NA12878. If you'd be willing to share a slide or two, either we or you may present it at our workshop. If you're interested, please email Justin Zook at NIST or respond to this email. Even if you just have a moment to write a couple sentences about how you're using them, it would be very helpful to let us know.

GIAB Use Case: Variant Callers Matter

With sequencing technologies and bioinformatics rapidly evolving, want to highlight some interesting use cases for our high-confidence calls for the pilot NIST Genome in a Bottle (GIAB) Reference Material, based on NA12878 (see ftp://ftp-trace.ncbi.nih.gov/giab/ftp/data/NA12878/variant_calls/NIST).  Our recent Nature Biotechnology paper (

Registration Open for GIAB Workshop August 14-15 in Gaithersburg, MD

You are all invited to the next Genome in a Bottle Workshop to be held at NIST (100 Bureau Dr, Gaithersburg, MD) on August 14-15, 2014. This will be a public workshop open to anyone interested in participating in the Genome in a Bottle work. An agenda will be sent out later, but our current plan for times is 9am to 5:30pm on August 14 and 9am to 12:45pm on August 15, followed by a steering committee meeting from 1pm to 2:30pm.

GIAB Workshop August 14-15 in Gaithersburg, MD

You are all invited to the next Genome in a Bottle Workshop to be held at NIST (100 Bureau Dr, Gaithersburg, MD) on August 14-15, 2014. This will be a public workshop open to anyone interested in participating in the Genome in a Bottle work. An agenda will be sent out later, but our current plan for times is 9am to 5:30pm on August 14 and 9am to 12:45pm on August 15, followed by a steering committee meeting from 1pm to 2:30pm.

Performance Metrics Specification Draft Available for Comment

In the January Genome in a Bottle workshop, the Performance Metrics Working Group decided to develop a specification for a “user interface” for the NIST whole genome Reference Materials. This specification is intended to standardize how performance metrics are calculated when a user compares their characterization of the Reference Materials to the benchmark genotypes developed by GIAB.

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