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.borroto@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:
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:
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 <Praveen.s@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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