---
course: NGS for evolutionary biologists: from basic scripting to variant calling
title: Tutorial - Variant calling, filtering - exercises
requires:
author: Chiara Batini, Pille Hallast
credits: Matthew Blades, Kate Lee (BBASH, University of Leicester, UK)
time:
---Each stage of the workflow will be described in terms of what is being done and the command required to run the software. Commands will be in the following format:
>$ command you need to type to run the software
Where:
>$ is the command prompt. The actual command prompt on your terminal will be in a format something like this:
[email protected]:[~]$
e.g in my case the command prompt looks like this:
[email protected]:[~]$
However, to save space in this manual I have replaced the actual command prompt with this:
>$ or removed at all.
The text in gray areas is the actual text you need to type into the command window to run the software. NOTE: After typing in a command, hit return to execute that command
A command is generally the name of the software to be used followed by a list of parameters and options for how the software should be run, e.g. the command below will run the software cutadapt. The text after cutadapt i.e. -a, -i and -o are all cutadapt parameters followed by their input values:
>$ cutadapt -a ATGAATCTA -i data_in.fastq -o data_out.fastq
NOTE: Be aware of spaces between text in commands as they are important!
During the practicals questions will be asked and a blank space left for you to fill in your answers. Questions are written in green text.