I agree, I prefer your solution, I will focus on that solution, thanks!
Although there is some software more or less used in the community such
Delly https://github.com/tobiasrausch/delly and Breakdancer
http://gmt.genome.wustl.edu/packages/breakdancer/documentation.html, that
doesn't use bed files, the only way to parallelize their execution is
through smaller bams

Regards


On 6 May 2015 at 15:00, Peter Cock <p.j.a.c...@googlemail.com> wrote:

> 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
> solution.
>
> Peter
>



-- 
Roberto Alonso
Functional Genomics Unit
Bioinformatics and Genomics Department
Prince Felipe Research Center (CIPF)
C./Eduardo Primo Yúfera (Científic), nº 3
(junto Oceanografico)
46012 Valencia, Spain
Tel: +34 963289680 Ext. 1021
Fax: +34 963289574
E-Mail: ralo...@cipf.es
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