Indeed, I have rewritten the code with the Peter suggestions and I was
thinking to update the PR with this code
On 6 May 2015 at 17:45, Joshua Udall wrote:
> Use subBam from the BamBam package. Written in C.
>
> subBam -g targets.bed sorted.bam -o sorted.subset.bam -m 0
>
> http://sourceforge.ne
Use subBam from the BamBam package. Written in C.
subBam -g targets.bed sorted.bam -o sorted.subset.bam -m 0
http://sourceforge.net/projects/bambam/
On Wed, May 6, 2015 at 4:23 AM, Peter Cock
wrote:
> Hi Roberto,
>
> Given the way BAM indexing works, I see no reason to actually
> split the BAM
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
On Wed, May 6, 2015 at 11:33 AM, Roberto Alonso CIPF 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
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 anoth
Hi Roberto,
Given the way BAM indexing works, I see no reason to actually
split the BAM file at all - it seems like wasted disk IO.
Instead, can you split a BED file into sub-regions? This way
each child GATK job would look at the full BAM file but only for
a small region described in the split B
Hello,
I have been working in the Galaxy parallelization module and I would like
to ask you some questions that I have about how to face one problem.
I have done one pull request about splitting bams:
https://github.com/galaxyproject/galaxy/pull/184
Regarding this, I think it is useful but it cou
