On Friday, December 3rd, at 8:00 AM, after copious amounts of coffee, my friend, colleague, and perpetual workout buddy Stephen Turner will defend his thesis. Join us in room 206 of the Preston Research Building at Vanderbilt Medical Center for the auspicious occasion!Getting Genetics Done by Stephen Turner is licensed under a Creative Commons Attribution (CC BY) License.

Designer Jesse Dee has an entertaining presentation on Slideshare about how to use Powerpoint effectively (although Edward Tufte may assert that such a thing is impossible). These are all things we probably know, but just don't take into consideration enough when we're giving a presentation. According to Dee, the number one most common mistake is lack of preparation.

I'm working on imputing GWAS data to the 1000 Genomes Project data using MaCH. For the model estimation phase you only need ~200 individuals. Here's a one-line unix command that will pull out 200 samples at random from a binary pedigree .fam file called myfamfile.fam: for i in `cut -d ' ' -f 1-2  myfamfile.fam | sed s/\ /,/g`; do echo "$RANDOM $i"; done | sort |

A few months ago I showed you how to syntax-highlight R code using Github Gists for displaying R code on your blog or other online medium. The idea's really simple if you use blogger - head over to gist.github.com, paste in your R code, create a public "gist", hit "embed", then copy the javascript onto your blog.

Obtaining the probability that zero, one, or two alleles are shared identical by descent (IBD) is useful for many reasons in a GWAS analysis. A while back I showed you how to visualize sample relatedness using R and ggplot2, which requires IBD estimates. Using plink --genome uses IBS and allele frequencies to infer IBD.

Human Genetics / Biostatistics Associate Professor (and my first statistics teacher) Dr. Chun Li will be giving a talk Wednesday on a new measure of R² for continuous, binary, ordinal, and survival outcomes.

As I mentioned in my recap of the ASHG 1000 genomes tutorial, I'm doing to be imputing some of my own data to 1000 genomes, and I'll try to post lessons learned along the way here under the 1000 genomes and imputation tags. I'm starting from a binary pedigree format file (plink's bed/bim/fam format) and the first thing in the 1000 genomes imputation cookbook is to store your data in Merlin format, one per chromosome.

If you missed the tutorial on the 1000 genomes project data last week at ASHG, you can now watch the tutorials on youtube and download the slides online at http://genome.gov/27542240.

As this year's ASHG meeting starts to wind down be sure to check out Variable Genome where Larry Parnell is summarizing what's going on at the talks he's been to. Also see the commentary on Genetic Inference by Luke Jostins. The 1000 Genomes tutorial from Wednesday night will be made available on genome.gov soon, and the presidential address, plenary sessions, and distinguished speaker symposium talks were recorded and will also soon be online.

Seminar announcement for Vanderbilt folks: Vanderbilt-Ingram Cancer Center Quantitative Sciences Seminar Series Presents Reproducible Research in the Omics Era: A Presentation and Panel Discussion Kevin R. Coombes, PhD Deputy Chair, Bioinformatics, and Professor of Bioinformatics and Computational BiologyM.D. Anderson Cancer Center and Keith Baggerly, PhD Associate Professor, Dept.

Pacific Biosciences is hosting a reception and dinner, and is screening their film The New Biology at this year's ASHG meeting.