Filter Reads Where Both A Read And Its Pair Is Unmapped.

Question

[Linda]

I have a bam file with all reads. I would like to filter out reads where both the read and its mate are unaligned. If either of them is aligned, I would like to keep both. Would

samtools view -F 12 file.bam

work?

Thanks,

Answer 1

[Leszek]

yes,

[?]

will throw away only those reads that are unmapped and their pair is unmapped as well.

[Istvan Albert]

I wonder of how the assumption of a mate's existence work - say if a read unmapped but the mate is missing - Is that considered as unmapped?

[Leszek]

To be honest, I don't know. you could specify -f 1 to take into account only paired reads. have a look here.

[Rm]

mate missing? it might not be possible unless paired reads are unequal?