Hi Raj,

I've been also testing GATK Beta pipeline on Galaxy. This is the workflow I
have so far:
http://test.g2.bx.psu.edu/u/cjav/w/gatk

There are a few error coming up that I haven't had the time to fix or work
around yet, but I think it could be a good starting point. For example an
issue with annotations in Variant Recalibrator tool, was recently fixed:
https://bitbucket.org/galaxy/galaxy-central/issue/682/variant-recalibrator-error-with

I haven't yet used the new manual method to enter annotations in the
workflow.

Regarding your questions, I don't have one for 1), I would love to hear
about a solution. In my case I'm working with RNA-seq data, so I think
everything would speed up if I use a good interval file, but is not clear
for me at the moment how to use it or when.

For 2), every time a tool outputs a BAM file in Galaxy, it is sorted and
indexed automatically, in fact even if the downstream tool can use a SAM
file, I still convert it to BAM just to make sure it is sorted and indexed.

Regards,
Carlos

On Thu, Dec 8, 2011 at 1:11 AM, Praveen Raj Somarajan <
pravee...@ocimumbio.com> wrote:

>  All,****
>
> ** **
>
> I'm using a locally installed galaxy with GATK 1.3 beta (recently
> updated). I would be interested in variant calling using GATK on both
> Illumina and SOLiD data. My questions are:****
>
> ** **
>
> 1) What should be the format that "Genomic Interval" option can accept in
> beta version. It produced an error when I provided an (enrichment coords)
> bed file? DepthOfCoverage had also produced error when I used bed files.
> Would beta release (v1.3) accept bed file as input for genomic intervals?*
> ***
>
> ** **
>
> 2) SAMtool index is seem to be missing in Galaxy. Is this true or any
> other module (say SAM->BAM) incorporates this functionality?****
>
> ** **
>
> Looking forward to your comments.****
>
> ** **
>
> Raj****
>
> ** **
>
> ** **
>
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