Removing Unmapped Reads from SAM File (SAMTools)

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?

samtools

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updated 6.8 years ago by swbarnes2

• written 6.8 years ago by gtasource

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

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written 6.8 years ago by GenoMax

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.

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written 6.8 years ago by gtasource

1 answer

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

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written 6.8 years ago by swbarnes2

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