Tim Webster and Alan Rogers are hosting the AGAR Workshop on Computational Genetics July 27-29, 2022. The workshop will focus on methods for inferring population history and admixture. It will be virtual, with lectures via Zoom and materials made available on github.
Applications are now closed.
We’ve set up a google group for communicating with participants. If you applied to the workshop, you should have received an invitation to join this group. If you accepted that invitation, you should be receiving posts.
Several people, who applied using their institutional email addresses, have had trouble accessing the google group. We’ve been fixing those problems by using alternate email addresses, such as gmail.
If you’re having problems of this sort, or if you haven’t received the emails described above, please get in touch: sregorra@gmail.com
We will meet each day from 9am-12pm and from 1-4pm, Mountain Daylight Time (UTC-6).
| Day | Time | Speaker | Topic |
|---|---|---|---|
| 2022-7-27 | AM | Ainash Childebayeva | Working with genomic data |
| 2022-7-27 | PM | Tim Webster | Building a reproducible pipeline to map reads and call variants |
| 2022-7-28 | AM | Colin Brand | Simulation with msprime |
| 2022-7-28 | PM | Shyamalika Gopalan | Introgression: background and theory |
| 2022-7-29 | AM | Robert Maier | Admixtools |
| 2022-7-29 | PM | Alan Rogers | Legofit |
echo $SHELL into your terminal.
If the result is /bin/bash, you’re all set. If not, see this tutorial for changing your
default shell.brew install r
brew install rstudio
at the bash prompt. Please familiarize yourself with how to change directories and source scripts in R.
git both to download the code and data for this
workshop, and also to install Legofit on your computer. See the
Legofit tutorial to find out how to install
git and Legofit. Once git is up and running, you can download the
agar22 repository as follows, using a bash terminal. First use cd
to move to the directory within which you want to install
agar22. Then typegit clone https://github.com/alanrogers/agar22.git agar22
When that has run, you should find a directory named “agar22”,
which contains all the files related to the workshop. As we make
changes to the workshop files, it’s easy to keep your own copy up
to date. Use cd to move into the agar22 directory and type
git pull
Chs. 4-5 of Lecture notes on gene genealogies
Rogers 2022 Using genetic data to build intuition about population history.
Colin Brand is a postdoc in the Capra Lab at UCSF. His current research focuses on characterizing adaptation and introgression in non-human primates and predicting phenotypes from genomic data in archaic hominins.
Ainash Childebayeva is in the Dept of Archaeogenetics, in the Max Planck Instute of Evolutionary Anthropology.
Shyamalika Gopalan is a postdoc in the Goldberg lab at Duke University. She has extensive experience using genetic data to infer population history.
Robert Maier is a Research Fellow at the Broad Institute, Harvard University. He is the lead developer of AdmixTools2, which he will teach during the workshop.
Alan Rogers is in the Anthro Dept of the University of Utah. He has developed several methods for inferring population history from genetic data. He will cover one of those methods, Legofit, during the workshop.
Tim Webster is in the Anthropology Department at the University of Utah. He uses genomic data and computational methods to understand primate evolution, ecology, and behavior. In particular, he explores (1) macroevolutionary processes, especially speciation, adaptation, and lineage-specific demographic history, (2) modern and historical aspects of behavioral ecology and social organization, and (3) sex chromosome evolution.