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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.

New high-confidence NA12878 genotypes integrating phased pedigree calls

We have recently been working to integrate the phased pedigree calls for NA12878 (from Real Time Genomics and Illumina Platinum Genomes) with the multiple dataset arbitration calls (from NIST and others in GIAB). Our integration process takes advantage of the strengths of each of these callsets to give a larger, more accurate set of phased high-confidence SNP, indel, and homozygous reference genotypes.

'How Well Did You Sequence that Genome?' NIST, Consortium Partners Have Answer

From the NIST Tech Beat newsletter issue of February 25, 2014 (http://www.nist.gov/mml/bbd/dna-022514.cfm)
Contact: Michael E. Newman, 301-975-3025, michael.newman@nist.gov

NIST-GIAB paper online in Nature Biotechnology

We are happy to announce that our paper "Integrating human sequence data sets provides a resource of benchmark SNP and indel genotype calls" is now published online in Nature Biotechnology at http://www.nature.com/nbt/journal/vaop/ncurrent/full/nbt.2835.html. For those of you using our NIST-GIAB high-confidence benchmark calls, we ask that you cite this manuscript rather than (or in addition to) our arXiv pre-print of this manuscript.

January 2014 Genome in a Bottle Workshop Summary and Slides

Thank you to all of you who attended our workshop January 27-28, 2014 at Stanford University. Your contributions to Genome in a Bottle are very much appreciated! Below, we have a summary of the topics discussed at the workshop, including links to slides with more details.

Update and Consortium Progress
- NIST plans to release its pilot whole genome Reference Material (RM 8398), based on a large batch of ~8000 vials of 10ug of NA12878 DNA from Coriell, by May 2014

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