On Wed, May 6, 2015 at 11:33 AM, Roberto Alonso CIPF <ralo...@cipf.es> wrote:
> Hello,
> I agree, what you say fits perfectly for GATK, but as I wanted to create a
> more generic code I did it this way (also because I am a newbie in the
> galaxy code and I didn't know so well how to implement this ). What about a
> tool that doesn't accept a region, just a bam? Maybe we can put another
> parameter in the parallelism tag that force to split the bam.
> Mostly, just to create a bed file would be better, right?
> What do you think?
> Regards

Maybe you're right - BAM splitting might be useful for some tools
(any examples?), even though BED splitting is a much more elegant

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