Finding unmapped reads using samtools

[Ash]

Hi guys,

Samtools is truly amazing! However, there's a couple of things I was wondering about...

Is there any way of pulling out those reads in a bam file, using samtools, where one pair of the read has mapped and the other pair of the read has not?

Or those reads where one pair of the read has mapped and the other mapped in a position that was not expected, say for example 5 or 10kb further upstream?

All help gratefully received!

A

[drio]

Study carefully the SAM specification, particularly the flag field. Once you know
what flag to use, go ahead and use the filter capabilities in samtools view (-f/-F INT)
to extract the reads you are interested on.

For example (show me reads where the mate is ummapped):

$  samtools view -f 8 foo.bam

[Ash]

Many thanks for your response drio. I think it may take me some time deciphering the intricacies of the flag field (a good few posts to read on this site!), so I'll be back with more dumb questions after this!

All the best,

A