Introduction

Ancestry components can be interesting to look at - ever wondered how they're calculated exactly? In this post - we'll look at one such tool called "qpAdm" which is the academic tool for making ancestry models. We'll be talking about it's installation and set up here mainly, testing models will come later.

Requirements

• A Linux based computer with 16 gigs of RAM
• Some knowledge of Unix commands

Walkthrough

1. Boot up your PC and get on your terminal.
2. Install git, base-devel, gsl and blas. The commands vary depending on what Linux distribution you're using.
3. If you are on Arch Linux, there's a package available in the AUR which you can directly install by typing

   yay -S admixtools-git

4. Even if you don't use Arch Linux, there's nothing to worry about, you can follow through the rest of the tutorial.
5. Run

   git clone https://github.com/DReichLab/AdmixTools.git

6. Once you're done with this run

   cd AdmixTools/src

7. Now you're in the right place directory. All we have to do is proceed with the actual install.
8. Next you run

   make clobber

9. You need admin access for this obviously. Enable sudo for your user and - run

   sudo make install

10. AdmixTools is installed now and you can run qpAdm, qpWave, convertf and other tools.

Post Install

1. The necessary install files should be there in the bin folder. You should type

   cd ..

   .
2. Now to test whether the instal worked or not,

   cd bin

3. and

   ./qpAdm

4. Now we set it up to work from any directory you want it in.
5. Type

   sudo cp * /usr/bin/

6. Test it by exiting the terminal and then opening a new one. And type:

   qpAdm

A Brief Guide

1. To test models, you need to build a parameter file. We'll post a detailed guide on this soon. For now check out the Harney et al 2021 supplementary.
2. To run qpAdm, you should cd into the directory that has your parameter file and then run

   qpAdm -p parfile.txt