Bioinformatics with Python Cookbook - Second Edition

Getting ready

You will need to run the first recipe in order to use the hapmap10_auto_noofs_ld binary PLINK file. Again, we will use a 10 percent subsampling of autosomes that have been LD-pruned with no offspring.

As in the second recipe, if you are not using Docker, you might not be able to use the code that I have produced; you can find these code files at https://github.com/tiagoantao/pygenomics. You can install it with the following command:

pip install pygenomics

In theory, for this recipe, you will need to download admixture (https://www.genetics.ucla.edu/software/admixture/). However, in this case, I will provide the outputs of running admixture on the HapMap data that we will use because running admixture takes a lot of time. You ...