about editing SAM/BAM files
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8.4 years ago
morovatunc ▴ 550

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

bam sam • 2.0k views
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8.4 years ago
tiago211287 ★ 1.4k

Check this biostars thread

Also, the samtools paper

Also, the sam format specification

Also, this

Also samtools manual

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

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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.

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

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