Hi all,
I was working on the integration of the "samtools view" to work with Galaxy.
The idea is to filter an indexed bam file on a chromosome with "samtools view
-bh in.bam.bai chr1".
After some research I noted that samtools will only execute this command when
it can find the corresponding so
On Wed, Jun 20, 2012 at 2:59 PM, wrote:
>
> Hi all,
>
> I was working on the integration of the "samtools view" to work with Galaxy.
> The idea is to filter an indexed bam file on a chromosome with "samtools
> view -bh in.bam.bai chr1".
> After some research I noted that samtools will only execut
: galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] samtools view region
On Wed, Jun 20, 2012 at 2:59 PM, wrote:
>
> Hi all,
>
> I was working on the integration of the "samtools view" to work with Galaxy.
> The idea is to filter an indexed bam file on a chromosome
Jaap,
I put a tool: "samtools_filter" into the galaxy toolshed
http://toolshed.g2.bx.psu.edu/
that uses samtools view to filter regions. It creates symbolic links as
Peter suggests.
(The symbolic links are created in the job_working directory which is
automatically deleted when the job i
