HI,

I need some help to start working with SAMtools. As a beginner with biostatistics background, it is my first time that I'm using Linux Ubuntu (I have installed it on my windows by making a machine on VMware for illustration purpose). Now I'm going to know how to work with SAMtools to carry out basic commands such as:

1- importing bam/sam files into samtools
2- Viewing the data
3- Sorting bam files
4. Calling variants

I have already searched on the internet and have found some tutorials such as http://www.htslib.org/doc/samtools.html , but I don't have any idea what those commands are!

could anybody please tell me where I can find a step by step tutorial for a beginner who even doesn't know how to read such commands?

If I am right, I should run samtools on terminal... by using the commands : "sudo apt-get install samtools" and then writing "samtools", I think I have run samtools but how should I write the commands in samtools on terminal?

I would also be grateful if someone tells me where I can find some low sized bam files to test samtools.

Thanks a lot!

Spend some time here learning the basics of [UNIX][1]. 
<br>
You can also take a look at the online materials for a NGS data analysis course that can be found [here][2]. This would give you an overall idea of steps you would need to learn and the materials for that.


  [1]: http://korflab.ucdavis.edu/Unix_and_Perl/current.html#part1
  [2]: http://angus.readthedocs.org/en/2014/