The presentation follows the narrative in the following html document:

• https://eriqande.github.io/con-gen-2021/bayes-mcmc-gtyperr-narrative.nb.html

Within that notebook are links to the Shiny Apps I have written to play with genotype likelihoods (as well as directions on how to use them). If you want to get the associated R project, you can go to my directory on the ConGen Box at:

• https://umt.box.com/s/n3x7v1hpqkf4h9glu41whxrqaostoqva

and then download the ngs-genotype-models directory.

Or, you can also just download it or clone it from GitHub:

• https://github.com/eriqande/ngs-genotype-models

Once you have that ngs-genotype-models directory you can open the RStudio project ngs-genotype-models.Rproj within the directory and then open any one of the Rmd documents in the top level directory (named 001-allele-freq-estimation.Rmd, 002-genotype-likelihoods-from-reads.Rmd and 003-read-inference-gsi.Rmd in RStudio). RStudio will prompt you to install any needed packages if you don’t already have them (namely tidyverse and shiny). After that, clicking the Run Document button at the top of the document will create a Shiny App for your Hands-On excercises.

These don’t run on the ConGen Shiny Server, so you have to run these on your personal computer.

And, only as a last resort, if you can’t get the Shiny Apps working in RStudio on your computer, you can visit their pages on shinyapps.io:

• https://eriqande.shinyapps.io/001-allele-freq-estimation/
• https://eriqande.shinyapps.io/002-genotype-likelihoods-from-reads/
• https://eriqande.shinyapps.io/003-read-inference-gsi/

I am expecting that the above will take most of the time we have together this morning, but if we have some leftover time, we could talk about gbs miscall rates in RAD data before probabilistic genotype calling was used, any my R package ‘whoa’.

Lecture slides for this:

https://eriqande.github.io/con-gen-2021/gbs-miscall.pdf

The computer practical accompanying this segment is in the box directory in the RStudio Project whoa-practical-session. This will run on the RStudio Server (if you move the whoa-practical-session directory to your own home directory). Fire it up and run through 001-whoa-first-steps.Rmd.