[Bioc-sig-seq] Loading large BAM files

[Kasper Daniel Hansen]

On Wed, Jul 13, 2011 at 4:36 PM, Ivan Gregoretti <ivangreg at gmail.com> wrote:
> Hi everybody,
>
> As I wait for my large BAM to be read in by scanBAM, I can't help but to wonder:
>
> Has anybody tried combining scanBam with multicore to load the
> chromosomes in parallel?
>
> That would require
>
> 1) to merge the chunks at the end and
>
> 2) the original BAM to be indexed.
>
> Does anybody have any experience to share?

Multicore will help if your task is cpu limited (and you can chunk
it).  However, your specific task is probably I/O limited, in which
case it is not clear that it would help to have more cores; in fact it
might be detrimental depending on your filesystem and hardware.

Kasper