samtools F option

[illinu]

Hi,

Can someone explain here what the -F option in samtools means?
-F INT Skip alignments with bits present in INTwhat does it mean an alignment with for example 4 bits and why would you want to skip it?

[sarvidsson]

Check the SAM specification, page 4 in http://samtools.github.io/hts-specs/SAMv1.pdf; the FLAG field bits can be filtered upon with samtools view -F/-f.
0x4 means unmapped - that way you can remove unaligned reads from your BAM (in a rather quick and dirty way, since you'll break half-mapped pairs).

[illinu]

This is the document I needed, the Manual doesnt explain much on this. Thank you

Is there a way to extract only paired unaligned reads?

[sarvidsson]

samtools view -f 13

should give you all completely non-aligning pairs as output; -F 13 would give you the inverse (all but the completely non-aligning pairs). At least on the GSNAP output data I happened to have at hand.

If the BAM contains a mixture of paired and single reads you might need several passes to retrieve all completely unmapped fragment sequences.