about editing SAM/BAM files

Question

[morovatunc]

Hello,

I am trying to learn sam tools for extracting the data of specific regions in SAM/BAM files from CG hub. So I will be looking for a specific regions in these files for numerous patients with a single cancer type. Could you advice me some sources about this topic because I would like to get advanced on this subject.

I looked for current biostars treads yet I have found one. Thus I apologise if there is an obvious one already.

Thank you for your help and advice.

Best regards,
Tunc

Answer 1

[tiago211287]

Check this biostars thread

Also, the samtools paper

Also, the sam format specification

Also, this

Also samtools manual

[Devon Ryan]

Moved this to an answer and gave a +1, since this is all the answer that's needed.

[sentausa]

And if you prefer to take a course, Coursera is offering a course called Command Line Tools for Genomic Data Science which also covers SAM/BAM and Samtools.

[morovatunc]

I finished the course in 2 days. Thank you for your advice it was very usefull for me.