3 Getting started

Before getting started, we need to discuss computers, specifically your computer. Most programs made to execute genetic epidemiology studies are developed for the Unix environment, for example Linux and macOS. Years ago - now I sound really old - when I just started out on my journey in genetic epidemiology, I had a fancy (no, really) Windows-laptop. So, stubborn as I was (am), I tried to make this work (I remember Jessica - see Epilogue 20 - warning against it) - I lost 3 months of my life. Then a friend of mine lend me his old MacBook - you know, really old, the beautiful white MacBook - and I was stunned. Everything worked. Instantly. Even on that old little white gem which was running OS X Leopard. I was sold. Until then I never understood why all those ‘gen epi’ people were always working on a Mac - I thought it was just a fashion statement. But, it is not. It is a necessity in our line of work.

So, take my advice, don’t waste your time. You think a MacBook is expensive? Time is the most precious commodity that we have - when it’s gone, it’s gone - you’ll never get it back. Money? You can make more. Invest in a MacBook, or get your employer to do so. Get a refurbished one - there are many great options out there. Everything in this practical primer you can do with the MacBook Air (from the 2010 generation and up) with 8Gb RAM and at least 256Gb hard drive. A refurbished MacBook would work just fine, you really don’t need the latest model.

Besides, those ‘gen epi’ programs may not work as intended in a Windows environment. Sure, Windows does allow users to install a linux subsystem within Windows 10+ and you can find the detail guide here. And you can create a virtual machine with Ubuntu installed) on your Windows-computer. But honestly, I wouldn’t bother.

This is not some elevator pitch to buy MacBook - in all other cases you’ll probably be fine without. But trust me, ‘gen epi’, and all other (academic) ‘office’ stuff you need to do, work like a charm on macOS.

For this practical every command is intended for Linux/macOS, in other words Unix-systems.

Next, I’ll briefly provide some background on the various programs that are commonly used Chapter 4.