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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

Availability of phase-consistent gold standard variant set for NA12878 and rtgTools software

I wanted to let you know of the availability of a gold standard variant data set for NA12878, NA12877 and their 11 offspring developed by RTG based on their consistency with the haplotype phases inferred for this family. Also available now is the free rtgTools package to allow comparisons of VCF calls with a gold standard.

Want to help characterize the first 4 PGP GIAB Reference Materials?

Several of you helped us to characterize the pilot candidate NIST Reference Material based on NA12878, and that data has started to be uploaded to our ftp site. We're starting to learn a lot of interesting things from this informal interlaboratory study about variability within and between labs and instruments. We are now asking for volunteers to characterize the next set of 4 candidate NIST Reference Materials from the Personal Genome Project.

Call for nominations for members of GIAB Steering Committee

Dear all,

In preparation for our upcoming Genome in a Bottle Consortium workshop January 27-28 at Stanford University, we would like to welcome nominations for Steering Committee members. To help make decisions for the priorities of the Consortium, we plan to have our first steering committee meeting at the end of the workshop from ~4pm to 5:30pm on January 28. If you would like to nominate yourself or someone else, please respond to this email or email Justin Zook and Marc Salit. Also, registration and an agenda for the upcoming workshop will be posted tomorrow.

New version of manuscript and highly confident genotypes for NA12878

We’ve uploaded a new version (v2.18) of our NIST highly confident snp and indel genotypes for NA12878 to the GIAB ftp site at NCBI (ftp://ftp-trace.ncbi.nih.gov/giab/ftp/data/NA12878/variant_calls/NIST). This new version contains some refinements around complex variant calling, and includes an Ion Proton whole genome sequencing dataset in the integration.

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