Extract reads from specific target in .bam file

Question

[Picasa]

Hi all,

I am looking to extract reads that are mapped to a specific target.

Let's say I have a file target.txt like this:

head target.txt

scaffold1

scaffold2

scaffold3

And an another file which is a bam file.

Is there a tool that extract reads (or filter) that have mapped only on my target ? ( I have one bam with paired reads and one bam with single reads).

[Pierre Lindenbaum]

samtools view -L your.bed your.bam