Re: [Samtools-help] Extract seq by seq name from bam file?

[Peter C. <p.j...@go...>]

On Fri, Apr 19, 2013 at 5:05 PM, Peng Yu <pen...@gm...> wrote:
> Hi,
>
> I want extract some sequences from bam file with known seq name. But I
> don't see there is such an option with samtools. Do I miss anything in
> the manual? Does anybody know what might be the best way extract
> sequences from bam files by sequence names? Thanks.
>

I've not got an off the shelf answer for you, but keep in mind with
paired end reads, multiple fragment reads, and multiple mappings
in general any one read name could return many SAM/BAM reads.

Peter