Variant calling with FreeBayes

In this recipe, we will see how to use an alignment file to call variants, or alterations in a genome. We will look at FreeBayes (https://github.com/freebayes/freebayes), which is a popular variant caller.In variant calling, we look at the pile-up of reads in the alignment and try to determine whether there are any variations from the reference sequence.Let’s take a look at an example:

Figure 5.10 – Variant Calling example (source: https://www.hammerlab.org/2015/01/23/faster-pileup-loading-with-bai-indices/)

Getting started

First, we will install FreeBayes using the following code. You may want to add it to your PATH:

! brew install freebayes

The code for this chapter can be found in Ch05/Ch05-4-variant-calling.ipynb.

How to do it...

Here are the steps to try this recipe:

1. First, we will import our libraries:

import subprocess
import os

1. Next, we define our run_command() function:

def run_command(cmd):
    print(f"Running:...