Thanks Carlos. For Q#1, I found something that GATK v1.3 does not explicity 
check the format of -L input file, hence the error. And the work around for 
commandline is to specify the format with -L, as shown below:

-L:bed <interval_coords.bed>

Any idea how to edit the wrapper code to resolve this issue in Galaxy? Has 
anybody experienced/resolved this before?

Thanks,

Raj.

From: Carlos Borroto [mailto:carlos.borr...@gmail.com]
Sent: Thursday, December 08, 2011 7:43 PM
To: Praveen Raj Somarajan
Cc: galaxy-user@lists.bx.psu.edu
Subject: Re: [galaxy-user] Genomic interval file for GATK

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<mailto: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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