Removing Unmapped Reads from SAM File (SAMTools)

Question

[gtasource]

I know, this question is everywhere. But I have yet to see somebody use the same samotols command as myself, and I wanted to double-check.

samtools view -S -f 4 aligned.sam > unmapped.sam

Yay?

[GenoMax]

Try it. If reads with a * in chromosome field are gone then you are all set.

[gtasource]

Just to clarify, the * in the chromosome signifies unmapped reads? So, in the above command, since I am extracting unmapped reads into a separate file, that file should have mostly reads with * in the chr field.

Answer 1

[swbarnes2]

Your way is fine. The -S is optional; the default behavior of samtools view is to output as sam, not bam.