Variant Discovery    ◾    115

collapsing bases in each position and identifying the most frequent base. In the figure, you

can notice how depth is important in determining the consensus base.

4.2.1.1  BCF Tools Variant Calling Pipeline

In the following, we will use BCFtools as a consensus variant caller to pileup and call vari-

ants. BCFtools [6] is a set of tools for the manipulation of variant in VCF files and its binary

form BCF. To download the latest BCFtools version, follow the installation instructions

available at “http://www.htslib.org/”. On Linux and Linux like platforms, you can also use

the following commands to install it:

sudo apt-get update -y

sudo apt-get install -y bcftools

Run the following commands on the Linux terminal to learn about

the usage and options of the “bcfools” and “bcftools mpileup”:

bcftools --help

bcftools mpileup

The general form for the variant calling is as follows:

FIGURE 4.2  Read alignment and a consensus sequence.