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!

It sounds like you are missing a lot of basic Unix knowledge that will make it difficult to progress without. If you are struggling with basic concepts such as terminal commands and their meaning, this will require you spend time and learn more about how to use a terminal in a Linux environment, and then spend some time reading the manual for the different programs you intend to use.

I'm going to go ahead and encourage you to think about using [Galaxy][1] for your project. It's a open, web-based platform for a variety of data analysis tasks and best of all features a GUI component for those that aren't very good or are rather new a terminal. [Here][2] seems to be a pretty good guide for variant calling using Galaxy, though admittedly i've never preformed this type of analysis so I cannot be entirely sure.

I also suggest that you somehow get a local machine with a copy of a Linux distro such as Ubuntu installed (perhaps ask your PI if this is possible), and not just a windows machine running a virtual machine. This will force you to get used to the Linux operating system and will make installing bioinformatic software such as samtools and eventually learning the terminal and the command line easier.

Here are a couple of links to get you started navigating the terminal and learning about the shell:

[Codeacademy][3]

[Command-Line Crash Course][4]

[Learning The Shell][5]

[Learn To Shell The Hard Way][6]


  [1]: https://galaxyproject.org/
  [2]: http://www.biomedcentral.com/content/supplementary/1756-0500-7-314-s1.pdf
  [3]: https://www.codecademy.com/learn/learn-the-command-line
  [4]: http://cli.learncodethehardway.org/book/
  [5]: http://linuxcommand.org/learning_the_shell.php
  [6]: http://learnpythonthehardway.org/book/appendix-a-cli/introduction.html