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.cock@googlemail.com> wrote:
On Wed, May 6, 2015 at 11:33 AM, Roberto Alonso CIPF <ralonso@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: ralonso@cipf.es