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!