/rfmix_tutorial

A short tutorial on local ancestry inference.

Primary LanguageC++

Using RFMix version 1.54.

Before running through the .ipynb tutorial, please check the following:

  1. I have provided two RFMix binaries in the folder binaries/ (for MacOS and Linux). Please move the appropriate one to the PopPhased/ folder prior to running the tutorial.
  2. Please ensure you have python2.7.
  3. Please unzip tutorial_data.zip.

On the off-chance that you can't run the executables or are otherwise having trouble, please move the outputPopPhased* files out of the example_output/ folder and into the same folder as the notebook. This way you should at least be able to visualize the local ancestry inference classification. You can also see the logfile of my RFMix run in this folder. (logfile_asw_rfprobs)`