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-e...
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:****
- 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?*
- 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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